Package: a4 Version: 1.52.0 Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting Suggests: MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats, hgu95av2.db License: GPL-3 Package: a4Base Version: 1.52.0 Depends: a4Preproc, a4Core Imports: methods, graphics, grid, Biobase, annaffy, mpm, genefilter, limma, multtest, glmnet, gplots Suggests: Cairo, ALL, hgu95av2.db, nlcv Enhances: gridSVG, JavaGD License: GPL-3 Package: a4Classif Version: 1.52.0 Depends: a4Core, a4Preproc Imports: methods, Biobase, ROCR, pamr, glmnet, varSelRF, utils, graphics, stats Suggests: ALL, hgu95av2.db, knitr, rmarkdown License: GPL-3 Package: a4Core Version: 1.52.0 Imports: Biobase, glmnet, methods, stats Suggests: knitr, rmarkdown License: GPL-3 Package: a4Preproc Version: 1.52.0 Imports: BiocGenerics, Biobase Suggests: ALL, hgu95av2.db, knitr, rmarkdown License: GPL-3 Package: a4Reporting Version: 1.52.0 Imports: methods, xtable Suggests: knitr, rmarkdown License: GPL-3 Package: ABarray Version: 1.72.0 Imports: Biobase, graphics, grDevices, methods, multtest, stats, tcltk, utils Suggests: limma, LPE License: GPL Package: abseqR Version: 1.22.0 Depends: R (>= 3.5.0) Imports: ggplot2, RColorBrewer, circlize, reshape2, VennDiagram, plyr, flexdashboard, BiocParallel (>= 1.1.25), png, grid, gridExtra, rmarkdown, knitr, vegan, ggcorrplot, ggdendro, plotly, BiocStyle, stringr, utils, methods, grDevices, stats, tools, graphics Suggests: testthat License: GPL-3 | file LICENSE Package: ABSSeq Version: 1.58.0 Depends: R (>= 2.10), methods Imports: locfit, limma Suggests: edgeR License: GPL (>= 3) Package: acde Version: 1.34.0 Depends: R(>= 3.3), boot(>= 1.3) Imports: stats, graphics Suggests: BiocGenerics, RUnit License: GPL-3 Package: ACE Version: 1.22.0 Depends: R (>= 3.4) Imports: Biobase, QDNAseq, ggplot2, grid, stats, utils, methods, grDevices, GenomicRanges Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 Package: aCGH Version: 1.82.0 Depends: R (>= 2.10), cluster, survival, multtest Imports: Biobase, grDevices, graphics, methods, stats, splines, utils License: GPL-2 Archs: x64 Package: ACME Version: 2.60.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), methods, BiocGenerics Imports: graphics, stats License: GPL (>= 2) Archs: x64 Package: ADaCGH2 Version: 2.44.0 Depends: R (>= 3.2.0), parallel, ff, GLAD Imports: bit, DNAcopy, tilingArray, waveslim, cluster, aCGH Suggests: CGHregions, Cairo, limma Enhances: Rmpi License: GPL (>= 3) Archs: x64 Package: ADAM Version: 1.20.0 Depends: R(>= 3.5), stats, utils, methods Imports: Rcpp (>= 0.12.18), GO.db (>= 3.6.0), KEGGREST (>= 1.20.2), knitr, pbapply (>= 1.3-4), dplyr (>= 0.7.6), DT (>= 0.4), stringr (>= 1.3.1), SummarizedExperiment (>= 1.10.1) LinkingTo: Rcpp Suggests: testthat, rmarkdown, BiocStyle License: GPL (>= 2) Archs: x64 Package: ADAMgui Version: 1.20.0 Depends: R(>= 3.6), stats, utils, methods, ADAM Imports: GO.db (>= 3.5.0), dplyr (>= 0.7.6), shiny (>= 1.1.0), stringr (>= 1.3.1), stringi (>= 1.2.4), varhandle (>= 2.0.3), ggplot2 (>= 3.0.0), ggrepel (>= 0.8.0), ggpubr (>= 0.1.8), ggsignif (>= 0.4.0), reshape2 (>= 1.4.3), RColorBrewer (>= 1.1-2), colorRamps (>= 2.3), DT (>= 0.4), data.table (>= 1.11.4), gridExtra (>= 2.3), shinyjs (>= 1.0), knitr, testthat Suggests: markdown, BiocStyle License: GPL (>= 2) Package: adductomicsR Version: 1.20.0 Depends: R (>= 3.6), adductData, ExperimentHub, AnnotationHub Imports: parallel (>= 3.3.2), data.table (>= 1.10.4), OrgMassSpecR (>= 0.4.6), foreach (>= 1.4.3), mzR (>= 2.14.0), ade4 (>= 1.7.6), rvest (>= 0.3.2), pastecs (>= 1.3.18), reshape2 (>= 1.4.2), pracma (>= 2.0.4), DT (>= 0.2), fpc (>= 2.1.10), doSNOW (>= 1.0.14), fastcluster (>= 1.1.22), RcppEigen (>= 0.3.3.3.0), bootstrap (>= 2017.2), smoother (>= 1.1), dplyr (>= 0.7.5), zoo (>= 1.8), stats (>= 3.5.0), utils (>= 3.5.0), graphics (>= 3.5.0), grDevices (>= 3.5.0), methods (>= 3.5.0), datasets (>= 3.5.0) Suggests: knitr (>= 1.15.1), rmarkdown (>= 1.5), Rdisop (>= 1.34.0), testthat License: Artistic-2.0 Package: ADImpute Version: 1.14.0 Depends: R (>= 4.0) Imports: checkmate, BiocParallel, data.table, DrImpute, kernlab, MASS, Matrix, methods, rsvd, S4Vectors, SAVER, SingleCellExperiment, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 + file LICENSE Package: adSplit Version: 1.74.0 Depends: R (>= 2.1.0), methods (>= 2.1.0) Imports: AnnotationDbi, Biobase (>= 1.5.12), cluster (>= 1.9.1), GO.db (>= 1.8.1), graphics, grDevices, KEGGREST (>= 1.30.1), multtest (>= 1.6.0), stats (>= 2.1.0) Suggests: golubEsets (>= 1.0), vsn (>= 1.5.0), hu6800.db (>= 1.8.1) License: GPL (>= 2) Archs: x64 Package: adverSCarial Version: 1.2.0 Imports: gtools, S4Vectors, methods, DelayedArray Suggests: knitr, RUnit, BiocGenerics, TENxPBMCData, CHETAH, stringr, LoomExperiment License: MIT + file LICENSE Package: AffiXcan Version: 1.22.0 Depends: R (>= 3.6), SummarizedExperiment Imports: MultiAssayExperiment, BiocParallel, crayon Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 Package: affxparser Version: 1.76.0 Depends: R (>= 2.14.0) Suggests: R.oo (>= 1.22.0), R.utils (>= 2.7.0), AffymetrixDataTestFiles License: LGPL (>= 2) Archs: x64 Package: affy Version: 1.82.0 Depends: R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5) Imports: affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods, preprocessCore, stats, utils, zlibbioc LinkingTo: preprocessCore Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools, hgu95av2cdf License: LGPL (>= 2.0) Archs: x64 Package: affycomp Version: 1.80.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3) Suggests: splines, affycompData License: GPL (>= 2) Package: affyContam Version: 1.62.0 Depends: R (>= 2.7.0), tools, methods, utils, Biobase, affy, affydata Suggests: hgu95av2cdf License: Artistic-2.0 Package: affycoretools Version: 1.76.0 Depends: Biobase, methods Imports: affy, limma, GOstats, gcrma, splines, xtable, AnnotationDbi, ggplot2, gplots, oligoClasses, ReportingTools, hwriter, lattice, S4Vectors, edgeR, RSQLite, BiocGenerics, DBI, Glimma Suggests: affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl, rmarkdown License: Artistic-2.0 Package: affyILM Version: 1.56.0 Depends: R (>= 2.10.0), methods, gcrma Imports: affxparser (>= 1.16.0), affy, graphics, Biobase Suggests: AffymetrixDataTestFiles, hgfocusprobe License: GPL-3 Package: affyio Version: 1.74.0 Depends: R (>= 2.6.0) Imports: zlibbioc, methods License: LGPL (>= 2) Archs: x64 Package: affylmGUI Version: 1.78.0 Imports: grDevices, graphics, stats, utils, tcltk, tkrplot, limma, affy, affyio, affyPLM, gcrma, BiocGenerics, AnnotationDbi, BiocManager, R2HTML, xtable License: GPL (>= 2) Package: affyPLM Version: 1.80.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), affy (>= 1.11.0), Biobase (>= 2.17.8), gcrma, stats, preprocessCore (>= 1.5.1) Imports: zlibbioc, graphics, grDevices, methods LinkingTo: preprocessCore Suggests: affydata, MASS, hgu95av2cdf License: GPL (>= 2) Archs: x64 Package: AffyRNADegradation Version: 1.50.0 Depends: R (>= 2.9.0), methods, affy Suggests: AmpAffyExample, hgu133acdf License: GPL-2 Package: AGDEX Version: 1.52.0 Depends: R (>= 2.10), Biobase, GSEABase Imports: stats License: GPL (>= 2) Package: aggregateBioVar Version: 1.14.0 Depends: R (>= 4.0) Imports: stats, methods, S4Vectors, SummarizedExperiment, SingleCellExperiment, Matrix, tibble, rlang Suggests: BiocStyle, magick, knitr, rmarkdown, testthat, BiocGenerics, DESeq2, magrittr, dplyr, ggplot2, cowplot, ggtext, RColorBrewer, pheatmap, viridis License: GPL-3 Package: agilp Version: 3.36.0 Depends: R (>= 2.14.0) License: GPL-3 Package: AgiMicroRna Version: 2.54.0 Depends: R (>= 2.10),methods,Biobase,limma,affy (>= 1.22),preprocessCore,affycoretools Imports: Biobase Suggests: geneplotter,marray,gplots,gtools,gdata,codelink License: GPL-3 Package: AHMassBank Version: 1.4.0 Depends: R (>= 4.2) Imports: AnnotationHubData (>= 1.5.24) Suggests: BiocStyle, knitr, AnnotationHub (>= 2.7.13), rmarkdown, methods, CompoundDb (>= 1.1.4) License: Artistic-2.0 Package: AIMS Version: 1.36.0 Depends: R (>= 2.10), e1071, Biobase Suggests: breastCancerVDX, hgu133a.db, RUnit, BiocGenerics License: Artistic-2.0 Package: airpart Version: 1.12.0 Depends: R (>= 4.1) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, scater, stats, smurf, apeglm (>= 1.13.3), emdbook, mclust, clue, dynamicTreeCut, matrixStats, dplyr, plyr, ggplot2, ComplexHeatmap, forestplot, RColorBrewer, rlang, lpSolve, grid, grDevices, graphics, utils, pbapply Suggests: knitr, rmarkdown, roxygen2 (>= 6.0.0), testthat (>= 3.0.0), gplots, tidyr License: GPL-2 Package: alabaster Version: 1.4.0 Depends: alabaster.base Imports: alabaster.matrix, alabaster.ranges, alabaster.se, alabaster.sce, alabaster.spatial, alabaster.string, alabaster.vcf, alabaster.bumpy, alabaster.mae Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE Package: alabaster.base Version: 1.4.2 Imports: alabaster.schemas, methods, utils, S4Vectors, rhdf5 (>= 2.47.6), jsonlite, jsonvalidate, Rcpp LinkingTo: Rcpp, Rhdf5lib Suggests: BiocStyle, rmarkdown, knitr, testthat, digest, Matrix License: MIT + file LICENSE Archs: x64 Package: alabaster.bumpy Version: 1.4.0 Depends: BumpyMatrix, alabaster.base Imports: methods, rhdf5, Matrix, BiocGenerics, S4Vectors, IRanges Suggests: BiocStyle, rmarkdown, knitr, testthat, jsonlite License: MIT + file LICENSE Package: alabaster.files Version: 1.2.0 Depends: alabaster.base, Imports: methods, S4Vectors, BiocGenerics, Rsamtools Suggests: BiocStyle, rmarkdown, knitr, testthat, VariantAnnotation, rtracklayer, Biostrings License: MIT + file LICENSE Package: alabaster.mae Version: 1.4.0 Depends: MultiAssayExperiment, alabaster.base Imports: methods, alabaster.se, S4Vectors, jsonlite, rhdf5 Suggests: testthat, knitr, SummarizedExperiment, BiocParallel, BiocStyle, rmarkdown License: MIT + file LICENSE Package: alabaster.matrix Version: 1.4.2 Depends: alabaster.base Imports: methods, BiocGenerics, S4Vectors, DelayedArray (>= 0.27.2), S4Arrays, SparseArray, rhdf5 (>= 2.47.1), HDF5Array, Matrix, Rcpp LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, chihaya, BiocSingular, ResidualMatrix License: MIT + file LICENSE Archs: x64 Package: alabaster.ranges Version: 1.4.2 Depends: GenomicRanges, alabaster.base Imports: methods, S4Vectors, BiocGenerics, IRanges, GenomeInfoDb, rhdf5 Suggests: testthat, knitr, BiocStyle, jsonlite License: MIT + file LICENSE Package: alabaster.sce Version: 1.4.0 Depends: SingleCellExperiment, alabaster.base Imports: methods, alabaster.se, jsonlite Suggests: knitr, testthat, BiocStyle, rmarkdown License: MIT + file LICENSE Package: alabaster.schemas Version: 1.4.0 Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE Package: alabaster.se Version: 1.4.1 Depends: SummarizedExperiment, alabaster.base Imports: methods, alabaster.ranges, alabaster.matrix, BiocGenerics, S4Vectors, IRanges, GenomicRanges, jsonlite Suggests: rmarkdown, knitr, testthat, BiocStyle License: MIT + file LICENSE Package: alabaster.spatial Version: 1.4.0 Depends: SpatialExperiment, alabaster.base Imports: methods, utils, grDevices, S4Vectors, alabaster.sce, rhdf5 Suggests: testthat, knitr, rmarkdown, BiocStyle, DropletUtils, magick, png, digest License: MIT + file LICENSE Package: alabaster.string Version: 1.4.0 Depends: Biostrings, alabaster.base Imports: utils, methods, S4Vectors Suggests: BiocStyle, rmarkdown, knitr, testthat License: MIT + file LICENSE Package: alabaster.vcf Version: 1.4.0 Depends: alabaster.base, VariantAnnotation Imports: methods, S4Vectors, alabaster.se, alabaster.string, Rsamtools Suggests: knitr, rmarkdown, BiocStyle, testthat License: MIT + file LICENSE Package: ALDEx2 Version: 1.36.0 Depends: methods, stats, zCompositions, lattice, latticeExtra Imports: Rfast, BiocParallel, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, multtest, directlabels Suggests: testthat, BiocStyle, knitr, rmarkdown, purrr, ggpattern, ggplot2, cowplot, tidyverse, magick License: GPL (>= 3) Package: alevinQC Version: 1.20.0 Depends: R (>= 4.0) Imports: rmarkdown (>= 2.5), tools, methods, ggplot2 (>= 3.4.0), GGally, dplyr, rjson, shiny, shinydashboard, DT, stats, utils, tximport (>= 1.17.4), cowplot, rlang, Rcpp LinkingTo: Rcpp Suggests: knitr, BiocStyle, testthat (>= 3.0.0), BiocManager License: MIT + file LICENSE Archs: x64 Package: AllelicImbalance Version: 1.42.0 Depends: R (>= 4.0.0), grid, GenomicRanges (>= 1.31.8), SummarizedExperiment (>= 0.2.0), GenomicAlignments (>= 1.15.6) Imports: methods, BiocGenerics, AnnotationDbi, BSgenome (>= 1.47.3), VariantAnnotation (>= 1.25.11), Biostrings (>= 2.47.6), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Rsamtools (>= 1.99.3), GenomicFeatures (>= 1.31.3), Gviz, lattice, latticeExtra, gridExtra, seqinr, GenomeInfoDb, nlme Suggests: testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown License: GPL-3 Package: AlphaBeta Version: 1.18.0 Depends: R (>= 3.6.0) Imports: dplyr (>= 0.7), data.table (>= 1.10), stringr (>= 1.3), utils (>= 3.6.0), gtools (>= 3.8.0), optimx (>= 2018-7.10), expm (>= 0.999-4), stats (>= 3.6), BiocParallel (>= 1.18), igraph (>= 1.2.4), graphics (>= 3.6), ggplot2 (>= 3.2), grDevices (>= 3.6), plotly (>= 4.9) Suggests: knitr, rmarkdown License: GPL-3 Package: AlphaMissenseR Version: 1.0.2 Depends: dplyr Imports: rjsoncons (>= 1.0.1), DBI, duckdb (>= 0.9.1), rlang, curl, BiocFileCache, spdl, memoise, BiocBaseUtils, utils, stats, methods, whisker Suggests: BiocManager, BiocGenerics, GenomicRanges, GenomeInfoDb, AnnotationHub, ensembldb, httr, tidyr, r3dmol, bio3d, shiny, colorspace, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 Package: AlpsNMR Version: 4.6.0 Depends: R (>= 4.2), future (>= 1.10.0) Imports: utils, generics, graphics, stats, grDevices, cli, magrittr (>= 1.5), dplyr (>= 1.1.0), signal (>= 0.7-6), rlang (>= 0.3.0.1), scales (>= 1.2.0), stringr (>= 1.3.1), tibble(>= 1.3.4), tidyr (>= 1.0.0), tidyselect, readxl (>= 1.1.0), purrr (>= 0.2.5), glue (>= 1.2.0), reshape2 (>= 1.4.3), mixOmics (>= 6.22.0), matrixStats (>= 0.54.0), fs (>= 1.2.6), rmarkdown (>= 1.10), speaq (>= 2.4.0), htmltools (>= 0.3.6), pcaPP (>= 1.9-73), ggplot2 (>= 3.1.0), baseline (>= 1.2-1), vctrs (>= 0.3.0), BiocParallel Suggests: BiocStyle, ChemoSpec, cowplot, curl, DT (>= 0.5), GGally (>= 1.4.0), ggrepel (>= 0.8.0), gridExtra, knitr, plotly (>= 4.7.1), progressr, SummarizedExperiment, S4Vectors, testthat (>= 2.0.0), writexl (>= 1.0), zip (>= 2.0.4) License: MIT + file LICENSE Package: altcdfenvs Version: 2.66.0 Depends: R (>= 2.7), methods, BiocGenerics (>= 0.1.0), S4Vectors (>= 0.9.25), Biobase (>= 2.15.1), affy, makecdfenv, Biostrings, hypergraph Suggests: plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db, hgu133acdf, Rgraphviz, RColorBrewer License: GPL (>= 2) Package: AMARETTO Version: 1.20.0 Depends: R (>= 3.6), impute, doParallel, grDevices, dplyr, methods, ComplexHeatmap Imports: callr (>= 3.0.0.9001), Matrix, Rcpp, BiocFileCache, DT, MultiAssayExperiment, circlize, curatedTCGAData, foreach, glmnet, httr, limma, matrixStats, readr, reshape2, tibble, rmarkdown, graphics, grid, parallel, stats, knitr, ggplot2, gridExtra, utils LinkingTo: Rcpp Suggests: testthat, MASS, knitr, BiocStyle License: Apache License (== 2.0) + file LICENSE Package: AMOUNTAIN Version: 1.30.0 Depends: R (>= 3.3.0) Imports: stats Suggests: BiocStyle, qgraph, knitr, rmarkdown License: GPL (>= 2) Archs: x64 Package: amplican Version: 1.26.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.22.0), Biostrings (>= 2.44.2), pwalign, data.table (>= 1.10.4-3) Imports: Rcpp, utils (>= 3.4.1), S4Vectors (>= 0.14.3), ShortRead (>= 1.34.0), IRanges (>= 2.10.2), GenomicRanges (>= 1.28.4), GenomeInfoDb (>= 1.12.2), BiocParallel (>= 1.10.1), gtable (>= 0.2.0), gridExtra (>= 2.2.1), ggplot2 (>= 3.3.4), ggthemes (>= 3.4.0), waffle (>= 0.7.0), stringr (>= 1.2.0), stats (>= 3.4.1), matrixStats (>= 0.52.2), Matrix (>= 1.2-10), dplyr (>= 0.7.2), rmarkdown (>= 1.6), knitr (>= 1.16), cluster (>= 2.1.4) LinkingTo: Rcpp Suggests: testthat, BiocStyle, GenomicAlignments License: GPL-3 Archs: x64 Package: Anaquin Version: 2.28.0 Depends: R (>= 3.3), ggplot2 (>= 2.2.0) Imports: ggplot2, ROCR, knitr, qvalue, locfit, methods, stats, utils, plyr, DESeq2 Suggests: RUnit, rmarkdown License: BSD_3_clause + file LICENSE Package: ANCOMBC Version: 2.6.0 Depends: R (>= 4.3.0) Imports: mia (>= 1.6.0), stats, CVXR, DescTools, Hmisc, MASS, Matrix, Rdpack, S4Vectors, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, doParallel, doRNG, energy, foreach, gtools, lme4, lmerTest, multcomp, nloptr, parallel, utils Suggests: dplyr, knitr, rmarkdown, testthat, DT, tidyr, tidyverse, microbiome, magrittr License: Artistic-2.0 Package: AneuFinder Version: 1.32.0 Depends: R (>= 3.5), GenomicRanges, ggplot2, cowplot, AneuFinderData Imports: methods, utils, grDevices, graphics, stats, foreach, doParallel, BiocGenerics (>= 0.31.6), S4Vectors, GenomeInfoDb, IRanges, Rsamtools, bamsignals, DNAcopy, ecp, Biostrings, GenomicAlignments, reshape2, ggdendro, ggrepel, mclust Suggests: knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 Archs: x64 Package: ANF Version: 1.26.0 Imports: igraph, Biobase, survival, MASS, stats, RColorBrewer Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat License: GPL-3 Package: animalcules Version: 1.20.0 Depends: R (>= 4.3.0) Imports: ape, assertthat, caret, covr, DESeq2, dplyr, DT, forcats, ggforce, ggplot2, GUniFrac, lattice, limma, magrittr, Matrix, methods, MultiAssayExperiment, plotly, rentrez, reshape2, ROCit, S4Vectors (>= 0.23.19), scales, shiny, shinyjs, stats, SummarizedExperiment, tibble, tidyr, tsne, umap, utils, vegan, XML Suggests: BiocStyle, biomformat, devtools, glmnet, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 Package: annaffy Version: 1.76.0 Depends: R (>= 2.5.0), methods, Biobase, BiocManager, GO.db Imports: AnnotationDbi (>= 0.1.15), DBI Suggests: hgu95av2.db, multtest, tcltk License: LGPL Package: annotate Version: 1.82.0 Depends: R (>= 2.10), AnnotationDbi (>= 1.27.5), XML Imports: Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics (>= 0.13.8), httr Suggests: hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit, BiocStyle, knitr License: Artistic-2.0 Package: AnnotationDbi Version: 1.66.0 Depends: R (>= 2.7.0), methods, stats4, BiocGenerics (>= 0.29.2), Biobase (>= 1.17.0), IRanges Imports: DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST Suggests: utils, hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr License: Artistic-2.0 Package: AnnotationFilter Version: 1.28.0 Depends: R (>= 3.4.0) Imports: utils, methods, GenomicRanges, lazyeval Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db, rmarkdown License: Artistic-2.0 Package: AnnotationForge Version: 1.46.0 Depends: R (>= 3.5.0), methods, utils, BiocGenerics (>= 0.15.10), Biobase (>= 1.17.0), AnnotationDbi (>= 1.33.14) Imports: DBI, RSQLite, XML, S4Vectors, RCurl Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db, markdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit License: Artistic-2.0 Package: AnnotationHub Version: 3.12.0 Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1) Imports: utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, httr, yaml, dplyr Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, txdbmaker, MSnbase, mzR, Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub Enhances: AnnotationHubData License: Artistic-2.0 Package: AnnotationHubData Version: 1.34.0 Depends: R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges (>= 2.3.23), GenomicRanges, AnnotationHub (>= 2.15.15) Imports: GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics, jsonlite, BiocManager, biocViews, BiocCheck, graph, AnnotationDbi, Biobase, Biostrings, DBI, GenomeInfoDb (>= 1.15.4), OrganismDbi, RSQLite, AnnotationForge, futile.logger (>= 1.3.0), XML, RCurl Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData, rmarkdown, HubPub License: Artistic-2.0 Package: annotationTools Version: 1.78.0 Imports: Biobase, stats Suggests: BiocStyle License: GPL Package: annotatr Version: 1.30.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures, GenomicRanges, GenomeInfoDb (>= 1.10.3), ggplot2, IRanges, methods, readr, regioneR, reshape2, rtracklayer, S4Vectors (>= 0.23.10), stats, utils Suggests: BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2, testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Ggallus.UCSC.galGal5.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene License: GPL-3 Package: anota Version: 1.52.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 Package: anota2seq Version: 1.26.0 Depends: R (>= 3.4.0), methods Imports: multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices, graphics, stats, utils, SummarizedExperiment Suggests: BiocStyle,knitr License: GPL-3 Package: antiProfiles Version: 1.44.0 Depends: R (>= 3.0), matrixStats (>= 0.50.0), methods (>= 2.14), locfit (>= 1.5) Suggests: antiProfilesData, RColorBrewer License: Artistic-2.0 Package: AnVIL Version: 1.16.1 Depends: R (>= 3.6), dplyr Imports: stats, utils, methods, futile.logger, jsonlite, httr, rapiclient (>= 0.1.3), yaml, tibble, tidyselect, tidyr, rlang, shiny, DT, miniUI, htmltools, BiocManager, BiocBaseUtils Suggests: parallel, knitr, rmarkdown, testthat, withr, readr, BiocStyle, devtools License: Artistic-2.0 Package: AnVILBilling Version: 1.14.0 Depends: R (>= 4.1) Imports: methods, DT, shiny, bigrquery, shinytoastr, DBI, magrittr, dplyr, lubridate, plotly, ggplot2 Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 Package: AnVILPublish Version: 1.14.0 Imports: AnVIL, BiocBaseUtils, BiocManager, httr, jsonlite, rmarkdown, yaml, readr, whisker, tools, utils, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 Package: AnVILWorkflow Version: 1.4.0 Depends: R (>= 4.2.0), Imports: utils, AnVIL, httr, methods, jsonlite, dplyr, tibble Suggests: knitr, BiocStyle License: Artistic-2.0 Package: APAlyzer Version: 1.18.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq2, ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2, methods, rtracklayer, VariantAnnotation, dplyr, tidyr, repmis, Rsamtools, HybridMTest Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, testthat, pasillaBamSubset License: LGPL-3 Package: apComplex Version: 2.70.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL Package: apeglm Version: 1.26.1 Imports: emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp LinkingTo: Rcpp, RcppEigen, RcppNumerical Suggests: DESeq2, airway, knitr, rmarkdown, testthat License: GPL-2 Archs: x64 Package: APL Version: 1.8.0 Depends: R (>= 4.2) Imports: reticulate, ggrepel, ggplot2, viridisLite, plotly, Seurat, SingleCellExperiment, magrittr, SummarizedExperiment, topGO, methods, stats, utils, org.Hs.eg.db, org.Mm.eg.db, rlang, Matrix Suggests: BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, testthat License: GPL (>= 3) Package: appreci8R Version: 1.22.0 Imports: shiny, shinyjs, DT, VariantAnnotation, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, Homo.sapiens, SNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, Biostrings, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.hs37d5, MafDb.gnomADex.r2.1.hs37d5, COSMIC.67, rentrez, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137, seqinr, openxlsx, Rsamtools, stringr, stats, GenomicRanges, S4Vectors, GenomicFeatures, IRanges, GenomicScores, SummarizedExperiment Suggests: GO.db, org.Hs.eg.db, utils License: LGPL-3 Package: aroma.light Version: 3.34.0 Depends: R (>= 2.15.2) Imports: stats, R.methodsS3 (>= 1.7.1), R.oo (>= 1.23.0), R.utils (>= 2.9.0), matrixStats (>= 0.55.0) Suggests: princurve (>= 2.1.4) License: GPL (>= 2) Package: ArrayExpress Version: 1.64.0 Depends: R (>= 2.9.0), Biobase (>= 2.4.0) Imports: oligo, limma, httr, utils, jsonlite, rlang, tools, methods Suggests: affy License: Artistic-2.0 Package: arrayMvout Version: 1.62.0 Depends: R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy Imports: mdqc, affyContam, lumi Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf License: Artistic-2.0 Package: arrayQuality Version: 1.82.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL Package: arrayQualityMetrics Version: 3.60.0 Imports: affy, affyPLM (>= 1.27.3), beadarray, Biobase, genefilter, graphics, grDevices, grid, gridSVG (>= 1.4-3), Hmisc, hwriter, lattice, latticeExtra, limma, methods, RColorBrewer, setRNG, stats, utils, vsn (>= 3.23.3), XML, svglite Suggests: ALLMLL, CCl4, BiocStyle, knitr License: LGPL (>= 2) Package: ARRmNormalization Version: 1.44.0 Depends: R (>= 2.15.1), ARRmData License: Artistic-2.0 Package: artMS Version: 1.22.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, bit64, circlize, cluster, corrplot, data.table, dplyr, getopt, ggdendro, ggplot2, gplots, ggrepel, graphics, grDevices, grid, limma, MSstats, openxlsx, org.Hs.eg.db, pheatmap, plotly, plyr, RColorBrewer, scales, seqinr, stats, stringr, tidyr, UpSetR, utils, VennDiagram, yaml Suggests: BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR, knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat License: GPL (>= 3) + file LICENSE Package: ASAFE Version: 1.30.0 Depends: R (>= 3.2) Suggests: knitr, testthat License: Artistic-2.0 Package: ASEB Version: 1.48.0 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) Archs: x64 Package: ASGSCA Version: 1.38.0 Imports: Matrix, MASS Suggests: BiocStyle License: GPL-3 Package: ASICS Version: 2.20.1 Depends: R (>= 3.5) Imports: BiocParallel, ggplot2, glmnet, grDevices, gridExtra, methods, mvtnorm, PepsNMR, plyr, quadprog, ropls, stats, SummarizedExperiment, utils, Matrix, zoo Suggests: knitr, rmarkdown, BiocStyle, testthat, ASICSdata License: GPL (>= 2) Package: ASpli Version: 2.14.0 Depends: methods, grDevices, stats, utils, parallel, edgeR, limma, AnnotationDbi Imports: GenomicRanges, GenomicFeatures, BiocGenerics, IRanges, GenomicAlignments, Gviz, S4Vectors, Rsamtools, BiocStyle, igraph, htmltools, data.table, UpSetR, tidyr, DT, MASS, grid, graphics, pbmcapply, txdbmaker License: GPL Package: AssessORF Version: 1.22.0 Depends: R (>= 3.5.0), DECIPHER (>= 2.10.0) Imports: Biostrings, GenomicRanges, IRanges, graphics, grDevices, methods, stats, utils Suggests: AssessORFData, BiocStyle, knitr, rmarkdown, RSQLite (>= 1.1) License: GPL-3 Package: ASSET Version: 2.22.0 Depends: R (>= 3.5.0), stats, graphics Imports: MASS, msm, rmeta Suggests: RUnit, BiocGenerics, knitr License: GPL-2 + file LICENSE Package: ASSIGN Version: 1.40.0 Depends: R (>= 3.4) Imports: gplots, graphics, grDevices, msm, Rlab, stats, sva, utils, ggplot2, yaml Suggests: testthat, BiocStyle, lintr, knitr, rmarkdown License: MIT + file LICENSE Package: ASURAT Version: 1.8.0 Depends: R (>= 4.0.0) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, Rcpp (>= 1.0.7), cluster, utils, plot3D, ComplexHeatmap, circlize, grid, grDevices, graphics LinkingTo: Rcpp Suggests: ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi, BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 + file LICENSE Archs: x64 Package: ATACCoGAPS Version: 1.6.0 Depends: R (>= 4.2.0), CoGAPS (>= 3.5.13) Imports: gtools, GenomicRanges, projectR, TFBSTools, GeneOverlap, msigdbr, tidyverse, gplots, motifmatchr, chromVAR, GenomicFeatures, IRanges, fgsea, rGREAT, JASPAR2016, Homo.sapiens, Mus.musculus, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, stringr, dplyr Suggests: knitr, viridis License: Artistic-2.0 Package: ATACseqQC Version: 1.28.0 Depends: R (>= 3.5.0), BiocGenerics, S4Vectors Imports: BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges, GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid, limma, Rsamtools (>= 1.31.2), randomForest, rtracklayer, stats, motifStack, preseqR, utils, KernSmooth, edgeR, BiocParallel Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat, rmarkdown License: GPL (>= 2) Package: ATACseqTFEA Version: 1.6.0 Depends: R (>= 4.2) Imports: BiocGenerics, S4Vectors, IRanges, Matrix, GenomicRanges, GenomicAlignments, GenomeInfoDb, SummarizedExperiment, Rsamtools, motifmatchr, TFBSTools, stats, pracma, ggplot2, ggrepel, dplyr, limma, methods, rtracklayer Suggests: BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC, rmarkdown, BiocStyle License: GPL-3 Package: atena Version: 1.10.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, MatrixGenerics, BiocParallel, S4Vectors, IRanges, GenomicFeatures, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub, matrixStats, cli Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit, TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer License: Artistic-2.0 Package: atSNP Version: 1.20.0 Depends: R (>= 3.6) Imports: BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table, ggplot2, grDevices, graphics, grid, motifStack, rappdirs, stats, testthat, utils, lifecycle LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 Archs: x64 Package: attract Version: 1.56.0 Depends: R (>= 3.4.0), AnnotationDbi Imports: Biobase, limma, cluster, GOstats, graphics, stats, reactome.db, KEGGREST, org.Hs.eg.db, utils, methods Suggests: illuminaHumanv1.db License: LGPL (>= 2.0) Package: AUCell Version: 1.26.0 Imports: DelayedArray, DelayedMatrixStats, data.table, graphics, grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats, SummarizedExperiment, BiocGenerics, utils Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 Package: autonomics Version: 1.12.1 Depends: R (>= 4.0) Imports: abind, BiocFileCache, BiocGenerics, bit64, codingMatrices, colorspace, data.table, dplyr, edgeR, ggforce, ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma, magrittr, matrixStats, methods, MultiAssayExperiment, parallel, RColorBrewer, rlang, R.utils, readxl, S4Vectors, scales, stats, stringi, SummarizedExperiment, tidyr, tidyselect, tools, utils, vsn Suggests: affy, AnnotationDbi, AnnotationHub, apcluster, BiocManager, BiocStyle, Biostrings, diagram, DBI, ensembldb, fpc, GenomicDataCommons, GenomicRanges, GEOquery, hgu95av2.db, ICSNP, jsonlite, knitr, lme4, lmerTest, MASS, mixOmics, mpm, nlme, OlinkAnalyze, org.Hs.eg.db, org.Mm.eg.db, pcaMethods, pheatmap, progeny, propagate, RCurl, RSQLite, remotes, rmarkdown, ropls, Rsubread, readODS, rtracklayer, statmod, survival, survminer, testthat, UniProt.ws, writexl, XML License: GPL-3 Package: AWFisher Version: 1.18.0 Depends: R (>= 3.6) Imports: edgeR, limma, stats Suggests: knitr, tightClust License: GPL-3 Archs: x64 Package: awst Version: 1.12.0 Imports: stats, methods, SummarizedExperiment Suggests: airway, ggplot2, testthat, EDASeq, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown License: MIT + file LICENSE Package: BaalChIP Version: 1.30.0 Depends: R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools, Imports: GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy, reshape2, scales, coda, foreach, ggplot2, methods, utils, graphics, stats Suggests: RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle License: Artistic-2.0 Package: bacon Version: 1.32.0 Depends: R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 License: GPL (>= 2) Archs: x64 Package: BADER Version: 1.42.0 Suggests: pasilla (>= 0.2.10) License: GPL-2 Archs: x64 Package: BadRegionFinder Version: 1.32.0 Imports: VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 Package: BAGS Version: 2.44.0 Depends: R (>= 2.10), breastCancerVDX, Biobase License: Artistic-2.0 Archs: x64 Package: ballgown Version: 2.36.0 Depends: R (>= 3.5.0), methods Imports: GenomicRanges (>= 1.17.25), IRanges (>= 1.99.22), S4Vectors (>= 0.9.39), RColorBrewer, splines, sva, limma, rtracklayer (>= 1.29.25), Biobase (>= 2.25.0), GenomeInfoDb Suggests: testthat, knitr, markdown License: Artistic-2.0 Package: bambu Version: 3.6.0 Depends: R(>= 4.1), SummarizedExperiment(>= 1.1.6), S4Vectors(>= 0.22.1), BSgenome, IRanges Imports: BiocGenerics, BiocParallel, data.table, dplyr, tidyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, stats, Rsamtools, methods, Rcpp, xgboost LinkingTo: Rcpp, RcppArmadillo Suggests: AnnotationDbi, Biostrings, rmarkdown, BiocFileCache, ggplot2, ComplexHeatmap, circlize, ggbio, gridExtra, knitr, testthat, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3), DESeq2, NanoporeRNASeq, purrr, apeglm, utils, DEXSeq Enhances: parallel License: GPL-3 + file LICENSE Archs: x64 Package: bamsignals Version: 1.36.0 Depends: R (>= 3.5.0) Imports: methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges, zlibbioc LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown License: GPL-2 Archs: x64 Package: BANDITS Version: 1.20.0 Depends: R (>= 4.3.0) Imports: Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel, foreach, methods, stats, graphics, ggplot2, DRIMSeq, BiocParallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings License: GPL (>= 3) Archs: x64 Package: bandle Version: 1.8.0 Depends: R (>= 4.1), S4Vectors, Biobase, MSnbase, pRoloc Imports: Rcpp (>= 1.0.4.6), pRolocdata, lbfgs, ggplot2, dplyr, plyr, knitr, methods, BiocParallel, robustbase, BiocStyle, ggalluvial, ggrepel, tidyr, circlize, graphics, stats, utils, grDevices, rlang LinkingTo: Rcpp, RcppArmadillo, BH Suggests: coda (>= 0.19-4), testthat, interp, fields, pheatmap, viridis, rmarkdown, spelling License: Artistic-2.0 Archs: x64 Package: Banksy Version: 1.0.0 Depends: R (>= 4.4.0) Imports: aricode, data.table, dbscan, SpatialExperiment, SingleCellExperiment, SummarizedExperiment, S4Vectors, stats, matrixStats, mclust, igraph, irlba, leidenAlg (>= 1.1.0), utils, uwot, RcppHungarian Suggests: knitr, rmarkdown, pals, scuttle, scater, scran, cowplot, ggplot2, testthat (>= 3.0.0), harmony, Seurat, ExperimentHub, spatialLIBD, BiocStyle License: file LICENSE Package: banocc Version: 1.28.0 Depends: R (>= 3.5.1), rstan (>= 2.17.4) Imports: coda (>= 0.18.1), mvtnorm, stringr Suggests: knitr, rmarkdown, methods, testthat, BiocStyle License: MIT + file LICENSE Package: barcodetrackR Version: 1.12.0 Depends: R (>= 4.1) Imports: cowplot, circlize, dplyr, ggplot2, ggdendro, ggridges, graphics, grDevices, magrittr, plyr, proxy, RColorBrewer, rlang, scales, shiny, stats, SummarizedExperiment, S4Vectors, tibble, tidyr, vegan, viridis, utils Suggests: BiocStyle, knitr, magick, rmarkdown, testthat License: file LICENSE Package: basecallQC Version: 1.28.0 Depends: R (>= 3.4), stats, utils, methods, rmarkdown, knitr, prettydoc, yaml Imports: ggplot2, stringr, XML, raster, dplyr, data.table, tidyr, magrittr, DT, lazyeval, ShortRead Suggests: testthat, BiocStyle License: GPL (>= 3) Package: BaseSpaceR Version: 1.48.0 Depends: R (>= 2.15.0), RCurl, RJSONIO Imports: methods Suggests: RUnit, IRanges, Rsamtools License: Apache License 2.0 Package: Basic4Cseq Version: 1.40.0 Depends: R (>= 3.4), Biostrings, GenomicAlignments, caTools, GenomicRanges, grDevices, graphics, stats, utils Imports: methods, RCircos, BSgenome.Ecoli.NCBI.20080805 Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 Package: BASiCS Version: 2.16.0 Depends: R (>= 4.2), SingleCellExperiment Imports: Biobase, BiocGenerics, coda, cowplot, ggExtra, ggplot2, graphics, grDevices, MASS, methods, Rcpp (>= 0.11.3), S4Vectors, scran, scuttle, stats, stats4, SummarizedExperiment, viridis, utils, Matrix (>= 1.5.0), matrixStats, assertthat, reshape2, BiocParallel, posterior, hexbin LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, magick License: GPL-3 Archs: x64 Package: BASiCStan Version: 1.6.0 Depends: R (>= 4.2), BASiCS, rstan (>= 2.18.1) Imports: methods, glmGamPoi, scran, scuttle, stats, utils, SingleCellExperiment, SummarizedExperiment, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstantools (>= 2.1.1) LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: testthat (>= 3.0.0), knitr, rmarkdown License: GPL-3 Archs: x64 Package: BasicSTARRseq Version: 1.32.0 Depends: GenomicRanges,GenomicAlignments Imports: S4Vectors,methods,IRanges,GenomeInfoDb,stats Suggests: knitr License: LGPL-3 Package: basilisk Version: 1.16.0 Depends: reticulate Imports: utils, methods, parallel, dir.expiry, basilisk.utils (>= 1.15.1) Suggests: knitr, rmarkdown, BiocStyle, testthat, callr License: GPL-3 Package: basilisk.utils Version: 1.16.0 Imports: utils, methods, tools, dir.expiry Suggests: reticulate, knitr, rmarkdown, BiocStyle, testthat, basilisk License: GPL-3 Package: batchelor Version: 1.20.0 Depends: SingleCellExperiment Imports: SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats, methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix, DelayedArray, DelayedMatrixStats, BiocParallel, scuttle, ResidualMatrix, ScaledMatrix, beachmat LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, scran, scater, bluster, scRNAseq License: GPL-3 Archs: x64 Package: BatchQC Version: 2.0.0 Depends: R (>= 4.3.0) Imports: data.table, DESeq2, dplyr, EBSeq, ggdendro, ggnewscale, ggplot2, limma, matrixStats, pheatmap, RColorBrewer, reader, reshape2, scran, shiny, stats, SummarizedExperiment, sva, tibble, tidyr, tidyverse, utils Suggests: BiocManager, BiocStyle, bladderbatch, dendextend, devtools, knitr, lintr, plotly, rmarkdown, shinythemes, spelling, testthat (>= 3.0.0) License: MIT + file LICENSE Package: BayesKnockdown Version: 1.30.0 Depends: R (>= 3.3) Imports: stats, Biobase License: GPL-3 Package: BayesSpace Version: 1.14.0 Depends: R (>= 4.0.0), SingleCellExperiment Imports: Rcpp (>= 1.0.4.6), stats, purrr, scater, scran, SummarizedExperiment, coda, rhdf5, S4Vectors, Matrix, assertthat, mclust, RCurl, DirichletReg, xgboost, utils, ggplot2, scales, BiocFileCache, BiocSingular LinkingTo: Rcpp, RcppArmadillo, RcppDist, RcppProgress Suggests: testthat, knitr, rmarkdown, igraph, spatialLIBD, dplyr, viridis, patchwork, RColorBrewer, Seurat License: MIT + file LICENSE Archs: x64 Package: bayNorm Version: 1.22.0 Depends: R (>= 3.5), Imports: Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, Matrix, parallel, MASS, locfit, fitdistrplus, stats, methods, graphics, grDevices, SingleCellExperiment, SummarizedExperiment, BiocParallel, utils LinkingTo: Rcpp, RcppArmadillo,RcppProgress Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat License: GPL (>= 2) Archs: x64 Package: baySeq Version: 2.38.0 Depends: R (>= 2.3.0), methods Imports: edgeR, GenomicRanges, abind, parallel, graphics, stats, utils Suggests: BiocStyle, BiocGenerics License: GPL-3 Package: BBCAnalyzer Version: 1.34.0 Imports: SummarizedExperiment, VariantAnnotation, Rsamtools, grDevices, GenomicRanges, IRanges, Biostrings Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 Package: BCRANK Version: 1.66.0 Depends: methods Imports: Biostrings Suggests: seqLogo License: GPL-2 Archs: x64 Package: bcSeq Version: 1.26.0 Depends: R (>= 3.4.0) Imports: Rcpp (>= 0.12.12), Matrix, Biostrings LinkingTo: Rcpp, Matrix Suggests: knitr License: GPL (>= 2) Archs: x64 Package: BDMMAcorrect Version: 1.22.0 Depends: R (>= 3.5), vegan, ellipse, ggplot2, ape, SummarizedExperiment Imports: Rcpp (>= 0.12.12), RcppArmadillo, RcppEigen, stats LinkingTo: Rcpp, RcppArmadillo, RcppEigen Suggests: knitr, rmarkdown, BiocGenerics License: GPL (>= 2) Archs: x64 Package: beachmat Version: 2.20.0 Imports: methods, DelayedArray (>= 0.27.2), SparseArray, BiocGenerics, Matrix, Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, rcmdcheck, BiocParallel, HDF5Array License: GPL-3 Archs: x64 Package: beachmat.hdf5 Version: 1.2.0 Imports: methods, beachmat, HDF5Array, DelayedArray, Rcpp LinkingTo: Rcpp, beachmat, Rhdf5lib Suggests: testthat, BiocStyle, knitr, rmarkdown, rhdf5, Matrix License: GPL-3 Archs: x64 Package: beadarray Version: 2.54.0 Depends: R (>= 2.13.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), hexbin Imports: BeadDataPackR, limma, AnnotationDbi, stats4, reshape2, GenomicRanges, IRanges, illuminaio, methods, ggplot2 Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr License: MIT + file LICENSE Archs: x64 Package: BeadDataPackR Version: 1.56.0 Imports: stats, utils Suggests: BiocStyle, knitr License: GPL-2 Archs: x64 Package: BEARscc Version: 1.24.0 Depends: R (>= 3.5.0) Imports: ggplot2, SingleCellExperiment, data.table, stats, utils, graphics, compiler Suggests: testthat, cowplot, knitr, rmarkdown, BiocStyle, NMF License: GPL-3 Package: BEAT Version: 1.42.0 Depends: R (>= 2.13.0) Imports: GenomicRanges, ShortRead, Biostrings, BSgenome License: LGPL (>= 3.0) Package: BEclear Version: 2.20.0 Depends: BiocParallel (>= 1.14.2) Imports: futile.logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp, abind, stats, graphics, utils, methods, dixonTest, ids LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, pander, seewave License: GPL-3 Archs: x64 Package: beer Version: 1.8.0 Depends: R (>= 4.2.0), PhIPData (>= 1.1.1), rjags Imports: cli, edgeR, BiocParallel, methods, progressr, stats, SummarizedExperiment, utils Suggests: testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr, rmarkdown, dplyr, ggplot2, spelling License: MIT + file LICENSE Package: benchdamic Version: 1.10.0 Depends: R (>= 4.3.0) Imports: stats, stats4, utils, methods, phyloseq, TreeSummarizedExperiment, BiocParallel, zinbwave, edgeR, DESeq2, limma, ALDEx2, corncob, SummarizedExperiment, MAST, Seurat, ANCOMBC, mixOmics, lme4, NOISeq, dearseq, MicrobiomeStat, Maaslin2, GUniFrac, metagenomeSeq, MGLM, ggplot2, RColorBrewer, plyr, reshape2, ggdendro, ggridges, graphics, cowplot, grDevices, tidytext Suggests: knitr, rmarkdown, kableExtra, BiocStyle, magick, SPsimSeq, testthat License: Artistic-2.0 Package: BERT Version: 1.0.0 Depends: R (>= 4.3.0) Imports: cluster, comprehenr, foreach (>= 1.5.2), invgamma, iterators (>= 1.0.14), janitor (>= 2.2.0), limma (>= 3.46.0), logging (>= 0.10-108), sva (>= 3.38.0), SummarizedExperiment, methods, BiocParallel Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle License: GPL-3 Package: betaHMM Version: 1.0.0 Depends: R (>= 4.3.0), SummarizedExperiment, S4Vectors, GenomicRanges Imports: stats, ggplot2, scales, methods, pROC, foreach, doParallel, parallel, cowplot, dplyr, tidyr, tidyselect, stringr, utils Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-3 Package: bettr Version: 1.0.0 Depends: R (>= 4.4.0) Imports: dplyr (>= 1.0), tidyr, ggplot2 (>= 3.4.1), shiny (>= 1.6), tibble, ComplexHeatmap, bslib, rlang, circlize, stats, grid, methods, cowplot, Hmisc, sortable, shinyjqui, grDevices, scales, DT, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: MIT + file LICENSE Package: BG2 Version: 1.4.0 Depends: R (>= 4.2.0) Imports: GA (>= 3.2), caret (>= 6.0-86), memoise (>= 1.1.0), Matrix (>= 1.2-18), MASS (>= 7.3-58.1), stats (>= 4.2.2) Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP, testthat (>= 3.0.0) License: GPL-3 + file LICENSE Package: BgeeCall Version: 1.20.0 Depends: R (>= 3.6) Imports: GenomicFeatures, tximport, Biostrings, rtracklayer, biomaRt, jsonlite, methods, dplyr, data.table, sjmisc, grDevices, graphics, stats, utils, rslurm, rhdf5 Suggests: knitr, testthat, rmarkdown, AnnotationHub, httr License: GPL-3 + file LICENSE Package: BgeeDB Version: 2.30.0 Depends: R (>= 3.6.0), topGO, tidyr Imports: R.utils, data.table, curl, RCurl, digest, methods, stats, utils, dplyr, RSQLite, graph, Biobase Suggests: knitr, BiocStyle, testthat, rmarkdown, markdown License: GPL-3 + file LICENSE Package: bgx Version: 1.70.0 Depends: R (>= 2.0.1), Biobase, affy (>= 1.5.0), gcrma (>= 2.4.1) Imports: Rcpp (>= 0.11.0) LinkingTo: Rcpp Suggests: affydata, hgu95av2cdf License: GPL-2 Archs: x64 Package: BHC Version: 1.56.0 License: GPL-3 Archs: x64 Package: BicARE Version: 1.62.0 Depends: R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase, GO.db Imports: methods Suggests: hgu95av2 License: GPL-2 Archs: x64 Package: BiFET Version: 1.24.0 Depends: R (>= 3.5.0) Imports: stats, poibin, GenomicRanges Suggests: rmarkdown, testthat, knitr License: GPL-3 Package: BiGGR Version: 1.40.0 Depends: R (>= 2.14.0), rsbml, hyperdraw, LIM,stringr Imports: hypergraph, limSolve License: file LICENSE Package: bigmelon Version: 1.30.0 Depends: R (>= 3.3), wateRmelon (>= 1.25.0), gdsfmt (>= 1.0.4), methods, minfi (>= 1.21.0), Biobase, methylumi Imports: stats, utils, GEOquery, graphics, BiocGenerics, illuminaio Suggests: BiocGenerics, RUnit, BiocStyle, minfiData, parallel, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter License: GPL-3 Package: BindingSiteFinder Version: 2.2.0 Depends: GenomicRanges, R (>= 4.2) Imports: tidyr, tibble, plyr, matrixStats, stats, ggplot2, methods, rtracklayer, S4Vectors, ggforce, GenomeInfoDb, ComplexHeatmap, RColorBrewer, lifecycle, rlang, forcats, dplyr, GenomicFeatures, IRanges, kableExtra, ggdist Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments, scales, Gviz, xlsx, GGally, patchwork, viridis, ggplotify, SummarizedExperiment, DESeq2, ggpointdensity, ggrastr, ashr License: Artistic-2.0 Package: bioassayR Version: 1.42.0 Depends: R (>= 3.5.0), DBI (>= 0.3.1), RSQLite (>= 1.0.0), methods, Matrix, rjson, BiocGenerics (>= 0.13.8) Imports: XML, ChemmineR Suggests: BiocStyle, RCurl, biomaRt, cellHTS2, knitr, knitcitations, knitrBootstrap, testthat, ggplot2, rmarkdown License: Artistic-2.0 Package: Biobase Version: 2.64.0 Depends: R (>= 2.10), BiocGenerics (>= 0.27.1), utils Imports: methods Suggests: tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr, limma License: Artistic-2.0 Archs: x64 Package: biobroom Version: 1.36.0 Depends: R (>= 3.0.0), broom Imports: dplyr, tidyr, Biobase Suggests: limma, DESeq2, airway, ggplot2, plyr, GenomicRanges, testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase, rmarkdown, SummarizedExperiment License: LGPL Package: biobtreeR Version: 1.16.0 Imports: httr, httpuv, stringi,jsonlite,methods,utils Suggests: BiocStyle, knitr,testthat,rmarkdown,markdown License: MIT + file LICENSE Package: bioCancer Version: 1.32.0 Depends: R (>= 3.6.0), radiant.data (>= 0.9.1), cBioPortalData, XML(>= 3.98) Imports: R.oo, R.methodsS3, DT (>= 0.3), dplyr (>= 0.7.2), tidyr, shiny (>= 1.0.5), AlgDesign (>= 1.1.7.3), import (>= 1.1.0), methods, AnnotationDbi, shinythemes, Biobase, geNetClassifier, org.Hs.eg.db, org.Bt.eg.db, DOSE, clusterProfiler, reactome.db, ReactomePA, DiagrammeR(<= 1.01), visNetwork, htmlwidgets, plyr, tibble, GO.db Suggests: BiocStyle, prettydoc, rmarkdown, knitr, testthat (>= 0.10.0) License: AGPL-3 | file LICENSE Package: BioCartaImage Version: 1.2.0 Depends: R (>= 4.3.0) Imports: magick, grid, stats, grDevices, utils Suggests: testthat, knitr, BiocStyle, ragg License: MIT + file LICENSE Package: BiocBaseUtils Version: 1.6.0 Depends: R (>= 4.2.0) Imports: methods, utils Suggests: knitr, rmarkdown, BiocStyle, tinytest License: Artistic-2.0 Package: BiocCheck Version: 1.40.0 Depends: R (>= 4.3.0) Imports: BiocBaseUtils, BiocFileCache, BiocManager, biocViews (>= 1.33.7), callr, codetools, graph, httr2, knitr, methods, rvest, stringdist, tools, utils Suggests: RUnit, BiocGenerics, Biobase, jsonlite, rmarkdown, downloader, devtools (>= 1.4.1), usethis, BiocStyle, GenomicRanges, gert License: Artistic-2.0 Package: BiocFHIR Version: 1.6.0 Depends: R (>= 4.2) Imports: DT, shiny, jsonlite, graph, tidyr, visNetwork, dplyr, utils, methods, BiocBaseUtils Suggests: knitr, testthat, rjsoncons, igraph, BiocStyle License: Artistic-2.0 Package: BiocFileCache Version: 2.12.0 Depends: R (>= 3.4.0), dbplyr (>= 1.0.0) Imports: methods, stats, utils, dplyr, RSQLite, DBI, filelock, curl, httr Suggests: testthat, knitr, BiocStyle, rmarkdown, rtracklayer License: Artistic-2.0 Package: BiocGenerics Version: 0.50.0 Depends: R (>= 4.0.0), methods, utils, graphics, stats Imports: methods, utils, graphics, stats Suggests: Biobase, S4Vectors, IRanges, GenomicRanges, DelayedArray, Biostrings, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2, flowClust, MSnbase, annotate, RUnit License: Artistic-2.0 Package: biocGraph Version: 1.66.0 Depends: Rgraphviz, graph Imports: Rgraphviz, geneplotter, graph, BiocGenerics, methods Suggests: fibroEset, geneplotter, hgu95av2.db License: Artistic-2.0 Package: BiocHubsShiny Version: 1.4.0 Depends: R (>= 4.3.0), shiny Imports: AnnotationHub, ExperimentHub, DT, htmlwidgets, S4Vectors, shinyAce, shinyjs, shinythemes, shinytoastr, utils Suggests: BiocManager, BiocStyle, knitr, rmarkdown, sessioninfo, shinytest2 License: Artistic-2.0 Package: BiocIO Version: 1.14.0 Depends: R (>= 4.3.0) Imports: BiocGenerics, S4Vectors, methods, tools Suggests: testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 Package: BiocNeighbors Version: 1.22.0 Imports: Rcpp, S4Vectors, BiocParallel, stats, methods, Matrix LinkingTo: Rcpp, RcppHNSW Suggests: testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy, RcppHNSW License: GPL-3 Archs: x64 Package: BiocOncoTK Version: 1.24.0 Depends: R (>= 3.6.0), methods, utils Imports: ComplexHeatmap, S4Vectors, bigrquery, shiny, stats, httr, rjson, dplyr, magrittr, grid, DT, GenomicRanges, IRanges, ggplot2, SummarizedExperiment, DBI, GenomicFeatures, curatedTCGAData, scales, ggpubr, plyr, car, graph, Rgraphviz, MASS, grDevices Suggests: knitr, dbplyr, org.Hs.eg.db, MultiAssayExperiment, BiocStyle, ontoProc, ontologyPlot, pogos, GenomeInfoDb, restfulSE (>= 1.3.7), BiocFileCache, TxDb.Hsapiens.UCSC.hg19.knownGene, Biobase, TxDb.Hsapiens.UCSC.hg18.knownGene, reshape2, testthat, AnnotationDbi, FDb.InfiniumMethylation.hg19, EnsDb.Hsapiens.v75, rmarkdown, rhdf5client, AnnotationHub License: Artistic-2.0 Package: BioCor Version: 1.28.0 Depends: R (>= 3.4.0) Imports: BiocParallel, GSEABase, Matrix, methods Suggests: airway, BiocStyle, boot, DESeq2, ggplot2 (>= 3.4.1), GOSemSim, Hmisc, knitr (>= 1.35), org.Hs.eg.db, reactome.db, rmarkdown, spelling, targetscan.Hs.eg.db, testthat (>= 3.0.0), WGCNA License: MIT + file LICENSE Package: BiocParallel Version: 1.38.0 Depends: methods, R (>= 3.5.0) Imports: stats, utils, futile.logger, parallel, snow, codetools LinkingTo: BH, cpp11 Suggests: BiocGenerics, tools, foreach, BBmisc, doParallel, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle, knitr, batchtools, data.table Enhances: Rmpi License: GPL-2 | GPL-3 Archs: x64 Package: BiocPkgTools Version: 1.22.0 Depends: htmlwidgets Imports: BiocFileCache, BiocManager, biocViews, tibble, magrittr, methods, rlang, stringr, stats, rvest, dplyr, xml2, readr, httr, htmltools, DT, tools, utils, igraph, jsonlite, gh, RBGL, graph, rorcid Suggests: BiocStyle, knitr, rmarkdown, testthat, tm, lubridate, networkD3, visNetwork, clipr, blastula, kableExtra, DiagrammeR, SummarizedExperiment License: MIT + file LICENSE Package: biocroxytest Version: 1.0.0 Depends: R (>= 4.4.0) Imports: cli, glue, roxygen2, stringr Suggests: BiocStyle, here, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) Package: BiocSet Version: 1.18.0 Depends: R (>= 3.6), dplyr Imports: methods, tibble, utils, rlang, plyr, S4Vectors, BiocIO, AnnotationDbi, KEGGREST, ontologyIndex, tidyr Suggests: GSEABase, airway, org.Hs.eg.db, DESeq2, limma, BiocFileCache, GO.db, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 Package: BiocSingular Version: 1.20.0 Imports: BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat LinkingTo: Rcpp, beachmat Suggests: testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix License: GPL-3 Archs: x64 Package: BiocSklearn Version: 1.26.0 Depends: R (>= 4.0), reticulate, methods, SummarizedExperiment Imports: basilisk Suggests: testthat, restfulSE, HDF5Array, BiocStyle, rmarkdown, knitr License: Artistic-2.0 Package: BiocStyle Version: 2.32.1 Imports: bookdown, knitr (>= 1.30), rmarkdown (>= 1.2), stats, utils, yaml, BiocManager Suggests: BiocGenerics, RUnit, htmltools License: Artistic-2.0 Package: biocthis Version: 1.14.0 Imports: BiocManager, fs, glue, rlang, styler, usethis (>= 2.0.1) Suggests: BiocStyle, covr, devtools, knitr, pkgdown, RefManageR, rmarkdown, sessioninfo, testthat, utils License: Artistic-2.0 Package: BiocVersion Version: 3.19.1 Depends: R (>= 4.4.0) License: Artistic-2.0 Package: biocViews Version: 1.72.0 Depends: R (>= 3.6.0) Imports: Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools, utils, XML, RCurl, RUnit, BiocManager Suggests: BiocGenerics, knitr, commonmark, BiocStyle License: Artistic-2.0 Package: BiocWorkflowTools Version: 1.30.0 Depends: R (>= 3.4) Imports: BiocStyle, bookdown, git2r, httr, knitr, rmarkdown, rstudioapi, stringr, tools, utils, usethis License: MIT + file LICENSE Package: biodb Version: 1.12.0 Depends: R (>= 4.1.0) Imports: BiocFileCache, R6, RCurl, RSQLite, Rcpp, XML, chk, git2r, jsonlite, lgr, lifecycle, methods, openssl, plyr, progress, rappdirs, stats, stringr, tools, withr, yaml LinkingTo: Rcpp, testthat Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, xml2 License: AGPL-3 Archs: x64 Package: biodbChebi Version: 1.10.0 Depends: R (>= 4.1) Imports: R6, biodb (>= 1.1.5) Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, lgr License: AGPL-3 Package: biodbExpasy Version: 1.8.0 Depends: R (>= 4.1) Imports: biodb (>= 1.3.1), R6, stringr, chk Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr License: AGPL-3 Package: biodbHmdb Version: 1.10.0 Depends: R (>= 4.1) Imports: R6, biodb (>= 1.3.2), Rcpp, zip LinkingTo: Rcpp, testthat Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, lgr License: AGPL-3 Archs: x64 Package: biodbKegg Version: 1.10.0 Depends: R (>= 4.1) Imports: R6, biodb (>= 1.4.2), chk, lifecycle Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, igraph, magick, lgr License: AGPL-3 Package: biodbLipidmaps Version: 1.10.0 Depends: R (>= 4.1) Imports: biodb (>= 1.3.2), lifecycle, R6 Suggests: BiocStyle, lgr, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr License: AGPL-3 Package: biodbNcbi Version: 1.8.0 Depends: R (>= 4.1) Imports: biodb (>= 1.3.2), R6, XML, chk Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr License: AGPL-3 Package: biodbNci Version: 1.8.0 Depends: R (>= 4.1) Imports: biodb (>= 1.3.1), R6, Rcpp, chk LinkingTo: Rcpp, testthat Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr License: AGPL-3 Archs: x64 Package: biodbUniprot Version: 1.10.0 Depends: R (>= 4.1.0) Imports: R6, biodb (>= 1.4.2) Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, lgr, covr License: AGPL-3 Package: bioDist Version: 1.76.0 Depends: R (>= 2.0), methods, Biobase,KernSmooth Suggests: locfit License: Artistic-2.0 Package: biomaRt Version: 2.60.1 Depends: methods Imports: utils, AnnotationDbi, progress, stringr, httr2, digest, BiocFileCache, rappdirs, xml2 Suggests: BiocStyle, knitr, mockery, rmarkdown, testthat, httptest2 License: Artistic-2.0 Package: biomformat Version: 1.32.0 Depends: R (>= 3.2), methods Imports: plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5 Suggests: testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6), rmarkdown (>= 0.7) License: GPL-2 Package: BioMVCClass Version: 1.72.0 Depends: R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz License: LGPL Package: biomvRCNS Version: 1.44.0 Depends: IRanges, GenomicRanges, Gviz Imports: methods, mvtnorm Suggests: cluster, parallel, GenomicFeatures, dynamicTreeCut, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) Archs: x64 Package: BioNAR Version: 1.6.0 Depends: R (>= 3.5.0), igraph (>= 2.0.1.1), poweRlaw, latex2exp, RSpectra, Rdpack Imports: stringr, viridis, clusterCons, fgsea, grid, methods, AnnotationDbi, dplyr, GO.db, org.Hs.eg.db (>= 3.19.1), rSpectral, WGCNA, ggplot2, ggrepel, minpack.lm, cowplot, data.table, scales, stats, Matrix Suggests: knitr, BiocStyle, magick, rmarkdown, igraphdata, testthat (>= 3.0.0), vdiffr, devtools, pander, plotly, randomcoloR License: Artistic-2.0 Package: BioNERO Version: 1.12.0 Depends: R (>= 4.1) Imports: WGCNA, dynamicTreeCut, ggdendro, matrixStats, sva, RColorBrewer, ComplexHeatmap, ggplot2, rlang, ggrepel, patchwork, reshape2, igraph, ggnetwork, intergraph, NetRep, stats, grDevices, utils, methods, BiocParallel, minet, GENIE3, SummarizedExperiment Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle, DESeq2, networkD3, covr License: GPL-3 Package: BioNet Version: 1.64.0 Depends: R (>= 2.10.0), graph, RBGL Imports: igraph (>= 1.0.1), AnnotationDbi, Biobase Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML License: GPL (>= 2) Package: BioQC Version: 1.32.0 Depends: R (>= 3.5.0), Biobase Imports: edgeR, Rcpp, methods, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, lattice, latticeExtra, rbenchmark, gplots, gridExtra, org.Hs.eg.db, hgu133plus2.db, ggplot2, reshape2, plyr, ineq, covr, limma, RColorBrewer License: GPL (>= 3) + file LICENSE Archs: x64 Package: biosigner Version: 1.32.0 Imports: Biobase, methods, e1071, grDevices, graphics, MultiAssayExperiment, MultiDataSet, randomForest, ropls, stats, SummarizedExperiment, utils Suggests: BioMark, BiocGenerics, BiocStyle, golubEsets, hu6800.db, knitr, omicade4, rmarkdown, testthat License: CeCILL Package: Biostrings Version: 2.72.1 Depends: R (>= 4.0.0), BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.31.2), XVector (>= 0.37.1), GenomeInfoDb Imports: methods, utils, grDevices, stats, crayon LinkingTo: S4Vectors, IRanges, XVector Suggests: graphics, pwalign, BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit, BiocStyle, knitr License: Artistic-2.0 Archs: x64 Package: BioTIP Version: 1.18.0 Depends: R (>= 3.6) Imports: igraph, cluster, psych, stringr, GenomicRanges, MASS, scran Suggests: knitr, markdown, base, rmarkdown, ggplot2 License: GPL-2 Package: biotmle Version: 1.28.0 Depends: R (>= 4.0) Imports: stats, methods, dplyr, tibble, ggplot2, ggsci, superheat, assertthat, drtmle (>= 1.0.4), S4Vectors, BiocGenerics, BiocParallel, SummarizedExperiment, limma Suggests: testthat, knitr, rmarkdown, BiocStyle, arm, earth, ranger, SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1) License: MIT + file LICENSE Package: biovizBase Version: 1.52.0 Depends: R (>= 3.5.0), methods Imports: grDevices, stats, scales, Hmisc, RColorBrewer, dichromat, BiocGenerics, S4Vectors (>= 0.23.19), IRanges (>= 1.99.28), GenomeInfoDb (>= 1.5.14), GenomicRanges (>= 1.23.21), SummarizedExperiment, Biostrings (>= 2.33.11), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), GenomicFeatures (>= 1.21.19), AnnotationDbi, VariantAnnotation (>= 1.11.4), ensembldb (>= 1.99.13), AnnotationFilter (>= 0.99.8), rlang Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit License: Artistic-2.0 Archs: x64 Package: BiRewire Version: 3.36.0 Depends: igraph, slam, Rtsne, Matrix Suggests: RUnit, BiocGenerics License: GPL-3 Archs: x64 Package: biscuiteer Version: 1.18.0 Depends: R (>= 4.1.0), biscuiteerData, bsseq Imports: readr, qualV, Matrix, impute, HDF5Array, S4Vectors, Rsamtools, data.table, Biobase, GenomicRanges, IRanges, BiocGenerics, VariantAnnotation, DelayedMatrixStats, SummarizedExperiment, GenomeInfoDb, Mus.musculus, Homo.sapiens, matrixStats, rtracklayer, QDNAseq, dmrseq, methods, utils, R.utils, gtools, BiocParallel Suggests: DSS, covr, knitr, rmarkdown, markdown, rlang, scmeth, pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10, BiocStyle License: GPL-3 Package: BiSeq Version: 1.44.0 Depends: R (>= 3.5.0), methods, S4Vectors, IRanges (>= 1.17.24), GenomicRanges, SummarizedExperiment (>= 0.2.0), Formula Imports: methods, BiocGenerics, Biobase, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, rtracklayer, parallel, betareg, lokern, Formula, globaltest License: LGPL-3 Package: blacksheepr Version: 1.18.0 Depends: R (>= 3.6) Imports: grid, stats, grDevices, utils, circlize, viridis, RColorBrewer, ComplexHeatmap, SummarizedExperiment, pasilla Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, curl License: MIT + file LICENSE Package: blima Version: 1.38.0 Depends: R(>= 3.3) Imports: beadarray(>= 2.0.0), Biobase(>= 2.0.0), Rcpp (>= 0.12.8), BiocGenerics, grDevices, stats, graphics LinkingTo: Rcpp Suggests: xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi, knitr License: GPL-3 Archs: x64 Package: BLMA Version: 1.28.0 Depends: ROntoTools, GSA, PADOG, limma, graph, stats, utils, parallel, Biobase, metafor, methods Suggests: RUnit, BiocGenerics License: GPL (>= 2) Package: BloodGen3Module Version: 1.12.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, ExperimentHub, methods, grid, graphics, stats, grDevices, circlize, testthat, ComplexHeatmap(>= 1.99.8), ggplot2, matrixStats, gtools, reshape2, preprocessCore, randomcoloR, V8, limma Suggests: RUnit, devtools, BiocGenerics, knitr, rmarkdown License: GPL-2 Package: bluster Version: 1.14.0 Imports: stats, methods, utils, cluster, Matrix, Rcpp, igraph, S4Vectors, BiocParallel, BiocNeighbors LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut, scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans, kohonen, apcluster, DirichletMultinomial, vegan, fastcluster License: GPL-3 Archs: x64 Package: bnbc Version: 1.26.0 Depends: R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment, GenomicRanges Imports: Rcpp (>= 0.12.12), IRanges, rhdf5, data.table, GenomeInfoDb, S4Vectors, matrixStats, preprocessCore, sva, parallel, EBImage, utils, HiCBricks LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, RUnit, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 Archs: x64 Package: bnem Version: 1.12.0 Depends: R (>= 4.1) Imports: CellNOptR, matrixStats, snowfall, Rgraphviz, cluster, flexclust, stats, RColorBrewer, epiNEM, mnem, Biobase, methods, utils, graphics, graph, affy, binom, limma, sva, vsn, rmarkdown Suggests: knitr, BiocGenerics, MatrixGenerics, BiocStyle, RUnit License: GPL-3 Package: BOBaFIT Version: 1.8.0 Depends: R (>= 2.10) Imports: dplyr, NbClust, ggplot2, ggbio, grDevices, stats, tidyr, GenomicRanges, ggforce, stringr, plyranges, methods, utils, magrittr Suggests: rmarkdown, markdown, BiocStyle, knitr, testthat (>= 3.0.0), utils, testthat License: GPL (>= 3) Package: borealis Version: 1.8.0 Depends: R (>= 4.2.0), Biobase Imports: doParallel, snow, purrr, plyr, foreach, gamlss, gamlss.dist, bsseq, methods, DSS, R.utils, utils, stats, ggplot2, cowplot, dplyr, rlang, GenomicRanges Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, annotatr, tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: GPL-3 Package: BPRMeth Version: 1.30.0 Depends: R (>= 3.5.0), GenomicRanges Imports: assertthat, methods, MASS, doParallel, parallel, e1071, earth, foreach, randomForest, stats, IRanges, S4Vectors, data.table, graphics, truncnorm, mvtnorm, Rcpp (>= 0.12.14), matrixcalc, magrittr, kernlab, ggplot2, cowplot, BiocStyle LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown License: GPL-3 | file LICENSE Archs: x64 Package: BRAIN Version: 1.50.0 Depends: R (>= 2.8.1), PolynomF, Biostrings, lattice License: GPL-2 Package: brainflowprobes Version: 1.18.0 Depends: R (>= 3.6.0) Imports: Biostrings (>= 2.52.0), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), bumphunter (>= 1.26.0), cowplot (>= 1.0.0), derfinder (>= 1.18.1), derfinderPlot (>= 1.18.1), GenomicRanges (>= 1.36.0), ggplot2 (>= 3.1.1), RColorBrewer (>= 1.1), utils, grDevices, GenomicState (>= 0.99.7) Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 2.1.0), covr License: Artistic-2.0 Package: branchpointer Version: 1.30.0 Depends: caret, R(>= 3.4) Imports: plyr, kernlab, gbm, stringr, cowplot, ggplot2, biomaRt, Biostrings, parallel, utils, stats, BSgenome.Hsapiens.UCSC.hg38, rtracklayer, GenomicRanges, GenomeInfoDb, IRanges, S4Vectors, data.table Suggests: knitr, BiocStyle License: BSD_3_clause + file LICENSE Package: breakpointR Version: 1.22.0 Depends: R (>= 3.5), GenomicRanges, cowplot, breakpointRdata Imports: methods, utils, grDevices, stats, S4Vectors, GenomeInfoDb (>= 1.12.3), IRanges, Rsamtools, GenomicAlignments, ggplot2, BiocGenerics, gtools, doParallel, foreach Suggests: knitr, BiocStyle, testthat License: file LICENSE Package: brendaDb Version: 1.18.0 Imports: dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel, crayon, utils, tidyr, grDevices, rlang, BiocFileCache, rappdirs LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, devtools License: MIT + file LICENSE Archs: x64 Package: BREW3R.r Version: 1.0.1 Imports: GenomicRanges, methods, rlang, S4Vectors, utils Suggests: testthat (>= 3.0.0), IRanges, knitr, rmarkdown, BiocStyle, rtracklayer License: GPL-3 Package: BridgeDbR Version: 2.14.0 Depends: R (>= 3.3.0), rJava Imports: curl Suggests: BiocStyle, knitr, rmarkdown, testthat License: AGPL-3 Package: BrowserViz Version: 2.26.0 Depends: R (>= 3.5.0), jsonlite (>= 1.5), httpuv(>= 1.5.0) Imports: methods, BiocGenerics Suggests: RUnit, BiocStyle, knitr, rmarkdown License: GPL-2 Package: BSgenome Version: 1.72.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.28), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.25.6), GenomicRanges (>= 1.31.10), Biostrings (>= 2.47.6), BiocIO, rtracklayer Imports: utils, stats, matrixStats, XVector, Rsamtools Suggests: BiocManager, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit, BSgenomeForge License: Artistic-2.0 Package: bsseq Version: 1.40.0 Depends: R (>= 4.0), methods, BiocGenerics, GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.19.5) Imports: IRanges (>= 2.23.9), GenomeInfoDb, scales, stats, graphics, Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors (>= 0.27.12), R.utils (>= 2.0.0), DelayedMatrixStats (>= 1.5.2), permute, limma, DelayedArray (>= 0.15.16), Rcpp, BiocParallel, BSgenome, Biostrings, utils, HDF5Array (>= 1.19.11), rhdf5 LinkingTo: Rcpp, beachmat Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat (>= 1.5.2), batchtools License: Artistic-2.0 Archs: x64 Package: BubbleTree Version: 2.34.0 Depends: R (>= 3.5), IRanges, GenomicRanges, plyr, dplyr, magrittr Imports: BiocGenerics (>= 0.31.6), BiocStyle, Biobase, ggplot2, WriteXLS, gtools, RColorBrewer, limma, grid, gtable, gridExtra, biovizBase, e1071, methods, grDevices, stats, utils Suggests: knitr, rmarkdown License: LGPL (>= 3) Package: BufferedMatrix Version: 1.68.0 Depends: R (>= 2.6.0), methods License: LGPL (>= 2) Archs: x64 Package: BufferedMatrixMethods Version: 1.68.0 Depends: R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods LinkingTo: BufferedMatrix Suggests: affyio, affy License: GPL (>= 2) Archs: x64 Package: bugsigdbr Version: 1.10.0 Depends: R (>= 4.1) Imports: BiocFileCache, methods, vroom, utils Suggests: BiocStyle, knitr, ontologyIndex, rmarkdown, testthat (>= 3.0.0) License: GPL-3 Package: BUMHMM Version: 1.28.0 Depends: R (>= 3.5.0) Imports: devtools, stringi, gtools, stats, utils, SummarizedExperiment, Biostrings, IRanges Suggests: testthat, knitr, BiocStyle License: GPL-3 Package: bumphunter Version: 1.46.0 Depends: R (>= 3.5), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), GenomeInfoDb, GenomicRanges, foreach, iterators, methods, parallel, locfit Imports: matrixStats, limma, doRNG, BiocGenerics, utils, GenomicFeatures, AnnotationDbi, stats Suggests: testthat, RUnit, doParallel, txdbmaker, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 Package: BumpyMatrix Version: 1.12.0 Imports: utils, methods, Matrix, S4Vectors, IRanges Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE Package: BUS Version: 1.60.0 Depends: R (>= 2.3.0), minet Imports: stats, infotheo License: GPL-3 Archs: x64 Package: BUScorrect Version: 1.22.0 Depends: R (>= 3.5.0) Imports: gplots, methods, grDevices, stats, SummarizedExperiment Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL (>= 2) Archs: x64 Package: BUSpaRse Version: 1.18.0 Depends: R (>= 3.6) Imports: AnnotationDbi, AnnotationFilter, biomaRt, BiocGenerics, Biostrings, BSgenome, dplyr, ensembldb, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, IRanges, magrittr, Matrix, methods, plyranges, Rcpp, S4Vectors, stats, stringr, tibble, tidyr, utils, zeallot LinkingTo: Rcpp, RcppArmadillo, RcppProgress, BH Suggests: knitr, rmarkdown, testthat, BiocStyle, txdbmaker, TENxBUSData, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 License: BSD_2_clause + file LICENSE Archs: x64 Package: BUSseq Version: 1.10.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots, grDevices, methods, stats, utils Suggests: BiocStyle, knitr, BiocGenerics License: Artistic-2.0 Archs: x64 Package: CaDrA Version: 1.2.0 Depends: R (>= 4.3.0) Imports: doParallel, ggplot2, gplots, graphics, grid, gtable, MASS, methods, misc3d, plyr, ppcor, R.cache, reshape2, stats, SummarizedExperiment Suggests: BiocManager, devtools, knitr, pheatmap, rmarkdown, testthat (>= 3.1.6) License: GPL-3 + file LICENSE Archs: x64 Package: CAEN Version: 1.12.0 Depends: R (>= 4.1) Imports: stats,PoiClaClu,SummarizedExperiment,methods Suggests: knitr,rmarkdown,BiocManager,SummarizedExperiment,BiocStyle License: GPL-2 Package: CAFE Version: 1.40.0 Depends: R (>= 2.10), biovizBase, GenomicRanges, IRanges, ggbio Imports: affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 Package: CAGEfightR Version: 1.24.0 Depends: R (>= 3.5), GenomicRanges (>= 1.30.1), rtracklayer (>= 1.38.2), SummarizedExperiment (>= 1.8.1) Imports: pryr(>= 0.1.3), assertthat(>= 0.2.0), methods(>= 3.6.3), Matrix(>= 1.2-12), BiocGenerics(>= 0.24.0), S4Vectors(>= 0.16.0), IRanges(>= 2.12.0), GenomeInfoDb(>= 1.14.0), GenomicFeatures(>= 1.29.11), GenomicAlignments(>= 1.22.1), BiocParallel(>= 1.12.0), GenomicFiles(>= 1.14.0), Gviz(>= 1.22.2), InteractionSet(>= 1.9.4), GenomicInteractions(>= 1.15.1) Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm9.knownGene License: GPL-3 + file LICENSE Package: cageminer Version: 1.10.0 Depends: R (>= 4.1) Imports: ggplot2, rlang, ggbio, ggtext, GenomeInfoDb, GenomicRanges, IRanges, reshape2, methods, BioNERO Suggests: testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle, rmarkdown, covr, sessioninfo License: GPL-3 Package: CAGEr Version: 2.10.0 Depends: methods, MultiAssayExperiment, R (>= 4.1.0) Imports: BiocGenerics, BiocParallel, BSgenome, CAGEfightR, data.table, DelayedArray, DelayedMatrixStats, formula.tools, GenomeInfoDb, GenomicAlignments, GenomicRanges (>= 1.37.16), ggplot2 (>= 2.2.0), gtools, IRanges (>= 2.18.0), KernSmooth, memoise, plyr, Rsamtools, reshape2, rtracklayer, S4Vectors (>= 0.27.5), som, stringdist, stringi, SummarizedExperiment, utils, vegan, VGAM Suggests: BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE, BiocStyle, knitr, rmarkdown License: GPL-3 Package: calm Version: 1.18.0 Imports: mgcv, stats, graphics Suggests: knitr, rmarkdown License: GPL (>= 2) Package: CAMERA Version: 1.60.0 Depends: R (>= 3.5.0), methods, Biobase, xcms (>= 1.13.5) Imports: methods, xcms, RBGL, graph, graphics, grDevices, stats, utils, Hmisc, igraph Suggests: faahKO, RUnit, BiocGenerics, multtest Enhances: Rmpi, snow License: GPL (>= 2) Archs: x64 Package: CaMutQC Version: 1.0.0 Depends: R (>= 4.0.0) Imports: ggplot2, dplyr, org.Hs.eg.db, vcfR, clusterProfiler, stringr, DT, MesKit, maftools, data.table, utils, stats, methods, tidyr Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 Package: canceR Version: 1.38.0 Depends: R (>= 4.3), tcltk, cBioPortalData Imports: GSEABase, tkrplot, geNetClassifier, RUnit, Formula, rpart, survival, Biobase, phenoTest, circlize, plyr, tidyr, dplyr, graphics, stats, utils, grDevices, R.oo, R.methodsS3 Suggests: testthat (>= 3.1), knitr, rmarkdown, BiocStyle License: GPL-2 Package: cancerclass Version: 1.48.0 Depends: R (>= 2.14.0), Biobase, binom, methods, stats Suggests: cancerdata License: GPL-3 Archs: x64 Package: CancerInSilico Version: 2.24.0 Depends: R (>= 3.4), Rcpp Imports: methods, utils, graphics, stats LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, BiocStyle, Rtsne, viridis, rgl, gplots License: GPL-2 Archs: x64 Package: CancerSubtypes Version: 1.30.0 Depends: R (>= 4.0), sigclust, NMF Imports: cluster, impute, limma, ConsensusClusterPlus, grDevices, survival Suggests: BiocGenerics, knitr, RTCGA.mRNA, rmarkdown License: GPL (>= 2) Package: cardelino Version: 1.6.0 Depends: R (>= 4.2), stats Imports: combinat, GenomeInfoDb, GenomicRanges, ggplot2, ggtree, Matrix, matrixStats, methods, pheatmap, snpStats, S4Vectors, utils, VariantAnnotation, vcfR Suggests: BiocStyle, foreach, knitr, pcaMethods, rmarkdown, testthat, VGAM Enhances: doMC License: GPL-3 Package: Cardinal Version: 3.6.3 Depends: R (>= 4.3), ProtGenerics, BiocGenerics, BiocParallel, S4Vectors (>= 0.27.3), methods, stats, stats4 Imports: CardinalIO, Biobase, EBImage, graphics, grDevices, irlba, Matrix, matter (>= 2.6.2), nlme, parallel, utils Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 Package: CardinalIO Version: 1.2.1 Depends: R (>= 4.3), matter, ontologyIndex Imports: methods, S4Vectors, stats, utils, tools Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 Archs: x64 Package: CARNIVAL Version: 2.14.0 Depends: R (>= 4.0) Imports: readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson, rmarkdown Suggests: RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0), sessioninfo License: GPL-3 Package: casper Version: 2.38.0 Depends: R (>= 3.6.0), Biobase, IRanges, methods, GenomicRanges Imports: BiocGenerics (>= 0.31.6), coda, EBarrays, gaga, gtools, GenomeInfoDb, GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer, S4Vectors (>= 0.9.25), sqldf, survival, VGAM Enhances: parallel License: GPL (>= 2) Archs: x64 Package: CATALYST Version: 1.28.0 Depends: R (>= 4.4), SingleCellExperiment Imports: circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot, data.table, dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel, ggridges, graphics, grDevices, grid, gridExtra, Matrix, matrixStats, methods, nnls, purrr, RColorBrewer, reshape2, Rtsne, SummarizedExperiment, S4Vectors, scales, scater, stats Suggests: BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat, uwot License: GPL (>= 2) Package: Category Version: 2.70.0 Depends: methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix Imports: utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGGREST, karyoploteR, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db License: Artistic-2.0 Package: categoryCompare Version: 1.48.0 Depends: R (>= 2.10), Biobase, BiocGenerics (>= 0.13.8), Imports: AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1), GOstats, annotate, colorspace, graph, RCy3 (>= 1.99.29), methods, grDevices, utils Suggests: knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter, rmarkdown License: GPL-2 Package: CausalR Version: 1.36.0 Depends: R (>= 3.2.0) Imports: igraph Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) Package: cbaf Version: 1.26.3 Depends: R (>= 4.1) Imports: BiocFileCache, RColorBrewer, cBioPortalData, genefilter, gplots, grDevices, stats, utils, openxlsx Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 Package: CBEA Version: 1.4.0 Depends: R (>= 4.2.0) Imports: BiocParallel, BiocSet, dplyr, lmom, fitdistrplus, magrittr, methods, mixtools, Rcpp (>= 1.0.7), stats, SummarizedExperiment, tibble, TreeSummarizedExperiment, tidyr, glue, generics, rlang, goftest LinkingTo: Rcpp Suggests: phyloseq, BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), tidyverse, roxygen2, mia, purrr License: MIT + file LICENSE Archs: x64 Package: cBioPortalData Version: 2.16.0 Depends: R (>= 4.2.0), AnVIL (>= 1.7.1), MultiAssayExperiment Imports: BiocFileCache (>= 1.5.3), digest, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, methods, readr, RaggedExperiment, RTCGAToolbox (>= 2.19.7), S4Vectors, SummarizedExperiment, stats, tibble, tidyr, TCGAutils (>= 1.9.4), utils Suggests: BiocStyle, knitr, survival, survminer, rmarkdown, testthat License: AGPL-3 Package: CBNplot Version: 1.4.0 Depends: R (>= 4.3.0) Imports: ggplot2, magrittr, graphite, ggraph, igraph, bnlearn (>= 4.7), patchwork, org.Hs.eg.db, clusterProfiler, utils, enrichplot, reshape2, ggforce, dplyr, tidyr, stringr, depmap, ExperimentHub, Rmpfr, graphlayouts, BiocFileCache, ggdist, purrr, pvclust, stats, rlang, oaqc Suggests: knitr, arules, concaveman, ReactomePA, bnviewer, DESeq2, GEOquery, rmarkdown, withr, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 Package: cbpManager Version: 1.12.0 Depends: shiny, shinydashboard Imports: utils, DT, htmltools, vroom, plyr, dplyr, magrittr, jsonlite, rapportools, basilisk, reticulate, shinyBS, shinycssloaders, rintrojs, rlang, markdown Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE Package: ccfindR Version: 1.24.0 Depends: R (>= 3.6.0) Imports: stats, S4Vectors, utils, methods, Matrix, SummarizedExperiment, SingleCellExperiment, Rtsne, graphics, grDevices, gtools, RColorBrewer, ape, Rmpi, irlba, Rcpp, Rdpack (>= 0.7) LinkingTo: Rcpp, RcppEigen Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) Archs: x64 Package: ccImpute Version: 1.6.0 Imports: Rcpp, matrixStats, stats, SIMLR, BiocParallel LinkingTo: Rcpp, RcppEigen Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater, SingleCellExperiment, mclust, testthat (>= 3.0.0) License: GPL-3 Archs: x64 Package: ccmap Version: 1.30.0 Imports: AnnotationDbi (>= 1.36.2), BiocManager (>= 1.30.4), ccdata (>= 1.1.2), doParallel (>= 1.0.10), data.table (>= 1.10.4), foreach (>= 1.4.3), parallel (>= 3.3.3), xgboost (>= 0.6.4), lsa (>= 0.73.1) Suggests: crossmeta, knitr, rmarkdown, testthat, lydata License: MIT + file LICENSE Package: CCPlotR Version: 1.2.0 Imports: plyr, tidyr, dplyr, ggplot2, forcats, ggraph, igraph, scatterpie, circlize, ComplexHeatmap, tibble, grid, ggbump, stringr, ggtext, ggh4x, patchwork, RColorBrewer, scales, viridis, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE Package: CCPROMISE Version: 1.30.0 Depends: R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase, utils License: GPL (>= 2) Package: ccrepe Version: 1.40.0 Imports: infotheo (>= 1.1) Suggests: knitr, BiocStyle, BiocGenerics, testthat, RUnit License: MIT + file LICENSE Package: CDI Version: 1.2.0 Depends: R(>= 3.6) Imports: matrixStats, Seurat, SeuratObject, stats, BiocParallel, ggplot2, reshape2, grDevices, ggsci, SingleCellExperiment, SummarizedExperiment, methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, magick, BiocStyle License: GPL-3 + file LICENSE Package: celaref Version: 1.22.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang, BiocGenerics, S4Vectors, readr, tibble, DelayedArray Suggests: limma, parallel, knitr, rmarkdown, ExperimentHub, testthat License: GPL-3 Package: celda Version: 1.20.0 Depends: R (>= 4.0), SingleCellExperiment, Matrix Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, methods, reshape2, S4Vectors, data.table, Rcpp, RcppEigen, uwot, enrichR, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, scater (>= 1.14.4), scran, dbscan, DelayedArray, stringr, ComplexHeatmap, gridExtra, circlize LinkingTo: Rcpp, RcppEigen Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData License: MIT + file LICENSE Archs: x64 Package: CellBarcode Version: 1.10.0 Depends: R (>= 4.1.0) Imports: methods, stats, Rcpp (>= 1.0.5), data.table (>= 1.12.6), plyr, ggplot2, stringr, magrittr, ShortRead (>= 1.48.0), Biostrings (>= 2.58.0), egg, Ckmeans.1d.dp, utils, S4Vectors, seqinr, zlibbioc, Rsamtools LinkingTo: Rcpp, BH Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown License: Artistic-2.0 Archs: x64 Package: cellbaseR Version: 1.28.0 Depends: R(>= 3.4) Imports: methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils, Rsamtools, BiocParallel, foreach, utils, parallel, doParallel Suggests: BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation License: Apache License (== 2.0) Package: CellBench Version: 1.20.0 Depends: R (>= 3.6), SingleCellExperiment, magrittr, methods, stats, tibble, utils Imports: assertthat, BiocGenerics, BiocFileCache, BiocParallel, dplyr, rlang, glue, memoise, purrr (>= 0.3.0), rappdirs, tidyr, tidyselect, lubridate Suggests: BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2 License: GPL-3 Package: cellHTS2 Version: 2.68.0 Depends: R (>= 2.10), RColorBrewer, Biobase, methods, genefilter, splots, vsn, hwriter, locfit, grid Imports: GSEABase, Category, stats4, BiocGenerics Suggests: ggplot2, GO.db License: Artistic-2.0 Package: CelliD Version: 1.12.0 Depends: R (>= 4.1), Seurat (>= 4.0.1), SingleCellExperiment Imports: Rcpp, RcppArmadillo, stats, utils, Matrix, tictoc, scater, stringr, irlba, data.table, glue, pbapply, umap, Rtsne, reticulate, fastmatch, matrixStats, ggplot2, BiocParallel, SummarizedExperiment, fgsea LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr, destiny, ggrepel License: GPL-3 + file LICENSE Archs: x64 Package: cellity Version: 1.32.0 Depends: R (>= 3.3) Imports: AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid, mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats, topGO, utils Suggests: BiocStyle, caret, knitr, testthat, rmarkdown License: GPL (>= 2) Package: CellMapper Version: 1.30.0 Depends: S4Vectors, methods Imports: stats, utils Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub License: Artistic-2.0 Package: cellmigRation Version: 1.12.0 Depends: R (>= 4.1), methods, foreach Imports: tiff, graphics, stats, utils, reshape2, parallel, doParallel, grDevices, matrixStats, FME, SpatialTools, sp, vioplot, FactoMineR, Hmisc Suggests: knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics, BiocManager, kableExtra, rgl License: GPL-2 Package: CellMixS Version: 1.20.0 Depends: kSamples, R (>= 4.0) Imports: BiocNeighbors, ggplot2, scater, viridis, cowplot, SummarizedExperiment, SingleCellExperiment, tidyr, magrittr, dplyr, ggridges, stats, purrr, methods, BiocParallel, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne License: GPL (>= 2) Package: CellNOptR Version: 1.50.0 Depends: R (>= 4.0.0), RBGL, graph, methods, RCurl, Rgraphviz, XML, ggplot2, rmarkdown Imports: igraph, stringi, stringr Suggests: data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics, Enhances: doParallel, foreach License: GPL-3 Archs: x64 Package: cellscape Version: 1.28.0 Depends: R (>= 3.3) Imports: dplyr (>= 0.4.3), gtools (>= 3.5.0), htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), reshape2 (>= 1.4.1), stringr (>= 1.0.0) Suggests: knitr, rmarkdown License: GPL-3 Package: CellScore Version: 1.24.0 Depends: R (>= 4.3.0) Imports: Biobase (>= 2.39.1), graphics (>= 3.5.0), grDevices (>= 3.5.0), gplots (>= 3.0.1), lsa (>= 0.73.1), methods (>= 3.5.0), RColorBrewer(>= 1.1-2), squash (>= 1.0.8), stats (>= 3.5.0), utils(>= 3.5.0), SummarizedExperiment Suggests: hgu133plus2CellScore, knitr, testthat (>= 3.0.0) License: GPL-3 Package: CellTrails Version: 1.22.0 Depends: R (>= 3.5), SingleCellExperiment Imports: BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats, ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv, reshape2, Rtsne, stats, splines, SummarizedExperiment, utils Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown License: Artistic-2.0 Package: cellxgenedp Version: 1.8.0 Depends: dplyr Imports: httr, curl, utils, tools, shiny, DT, rjsoncons Suggests: zellkonverter, SingleCellExperiment, HDF5Array, tidyr, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery License: Artistic-2.0 Package: CEMiTool Version: 1.28.0 Depends: R (>= 4.0) Imports: methods, scales, dplyr, data.table (>= 1.9.4), WGCNA, grid, ggplot2, ggpmisc, ggthemes, ggrepel, sna, clusterProfiler, fgsea, stringr, knitr, rmarkdown, igraph, DT, htmltools, pracma, intergraph, grDevices, utils, network, matrixStats, ggdendro, gridExtra, gtable, fastcluster Suggests: testthat, BiocManager License: GPL-3 Package: censcyt Version: 1.12.0 Depends: R (>= 4.0), diffcyt Imports: BiocParallel, broom.mixed, dirmult, dplyr, edgeR, fitdistrplus, lme4, magrittr, MASS, methods, mice, multcomp, purrr, rlang, S4Vectors, stats, stringr, SummarizedExperiment, survival, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2 License: MIT + file LICENSE Package: Cepo Version: 1.10.2 Depends: GSEABase, R (>= 4.1) Imports: DelayedMatrixStats, DelayedArray, HDF5Array, S4Vectors, methods, SingleCellExperiment, SummarizedExperiment, ggplot2, rlang, grDevices, patchwork, reshape2, BiocParallel, stats, dplyr, purrr Suggests: knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater, scMerge, fgsea, escape, pheatmap License: MIT + file LICENSE Package: ceRNAnetsim Version: 1.16.0 Depends: R (>= 4.0.0), dplyr, tidygraph Imports: furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr, future, stats Suggests: knitr, png, rmarkdown, testthat, covr License: GPL (>= 3.0) Package: CeTF Version: 1.16.0 Depends: R (>= 4.0) Imports: circlize, ComplexHeatmap, clusterProfiler, DESeq2, dplyr, GenomicTools.fileHandler, GGally, ggnetwork, ggplot2, ggpubr, ggrepel, graphics, grid, igraph, Matrix, network, Rcpp, RCy3, stats, SummarizedExperiment, S4Vectors, utils, methods LinkingTo: Rcpp, RcppArmadillo Suggests: airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat License: GPL-3 Archs: x64 Package: CexoR Version: 1.42.0 Depends: R (>= 4.2.0), S4Vectors, IRanges Imports: Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 | GPL-2 + file LICENSE Package: CFAssay Version: 1.38.0 Depends: R (>= 2.10.0) License: LGPL Package: cfdnakit Version: 1.2.0 Depends: R (>= 4.3) Imports: Biobase, dplyr, GenomicRanges, GenomeInfoDb, ggplot2, IRanges, magrittr, PSCBS, QDNAseq, Rsamtools, utils, S4Vectors, stats, rlang Suggests: rmarkdown, knitr, roxygen2, BiocStyle License: GPL-3 Package: cfDNAPro Version: 1.10.0 Depends: R (>= 4.1.0), magrittr (>= 1.5.0) Imports: tibble, GenomicAlignments, IRanges, plyranges, GenomeInfoDb, GenomicRanges, BiocGenerics, stats, utils, dplyr (>= 0.8.3), stringr (>= 1.4.0), quantmod (>= 0.4), ggplot2 (>= 3.2.1), Rsamtools (>= 2.4.0), rlang (>= 0.4.0), BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.NCBI.GRCh38 Suggests: scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools (>= 2.3.0), BiocStyle, testthat License: GPL-3 Package: cfTools Version: 1.4.0 Imports: Rcpp, utils, GenomicRanges, basilisk, R.utils, stats, cfToolsData LinkingTo: Rcpp, BH Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: file LICENSE Archs: x64 Package: CGEN Version: 3.40.0 Depends: R (>= 4.0), survival, mvtnorm Imports: stats, graphics, utils, grDevices Suggests: cluster License: GPL-2 + file LICENSE Archs: x64 Package: CGHbase Version: 1.64.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), marray License: GPL Package: CGHcall Version: 2.66.0 Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase (>= 1.15.1), snowfall Package: cghMCR Version: 1.62.0 Depends: methods, DNAcopy, CNTools, limma Imports: BiocGenerics (>= 0.1.6), stats4 License: LGPL Package: CGHnormaliter Version: 1.58.0 Depends: CGHcall (>= 2.17.0), CGHbase (>= 1.15.0) Imports: Biobase, CGHbase, CGHcall, methods, stats, utils License: GPL (>= 3) Package: CGHregions Version: 1.62.0 Depends: R (>= 2.0.0), methods, Biobase, CGHbase Package: ChAMP Version: 2.34.0 Depends: R (>= 3.3), minfi, ChAMPdata (>= 2.6.0),DMRcate, Illumina450ProbeVariants.db,IlluminaHumanMethylationEPICmanifest, DT, RPMM Imports: prettydoc,Hmisc,globaltest,sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b4.hg19, limma, DNAcopy, preprocessCore,impute, marray, wateRmelon, plyr,goseq,missMethyl,kpmt,ggplot2, GenomicRanges,qvalue,isva,doParallel,bumphunter,quadprog,shiny,shinythemes,plotly (>= 4.5.6),RColorBrewer,dendextend, matrixStats,combinat Suggests: knitr,rmarkdown License: GPL-3 Package: ChemmineOB Version: 1.42.0 Depends: R (>= 2.15.1), methods Imports: BiocGenerics, zlibbioc, Rcpp (>= 0.11.0) LinkingTo: BH, Rcpp, zlibbioc Suggests: ChemmineR, BiocStyle, knitr, knitrBootstrap, BiocManager, rmarkdown,RUnit Enhances: ChemmineR (>= 2.13.0) License: Artistic-2.0 Archs: x64 Package: ChemmineR Version: 3.56.0 Depends: R (>= 2.10.0), methods Imports: rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp (>= 0.11.0), ggplot2,grid,gridExtra, png,base64enc,DT,rsvg,jsonlite,stringi LinkingTo: Rcpp, BH Suggests: RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs, png,rmarkdown, BiocManager,bibtex Enhances: ChemmineOB License: Artistic-2.0 Archs: x64 Package: CHETAH Version: 1.20.0 Depends: R (>= 4.2), ggplot2, SingleCellExperiment Imports: shiny, plotly, pheatmap, bioDist, dendextend, cowplot, corrplot, grDevices, stats, graphics, reshape2, S4Vectors, SummarizedExperiment Suggests: knitr, rmarkdown, Matrix, testthat, vdiffr License: file LICENSE Package: Chicago Version: 1.32.0 Depends: R (>= 3.3.1), data.table Imports: matrixStats, MASS, Hmisc, Delaporte, methods, grDevices, graphics, stats, utils Suggests: argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub License: Artistic-2.0 Package: chihaya Version: 1.4.0 Depends: DelayedArray Imports: methods, Matrix, rhdf5, Rcpp, HDF5Array LinkingTo: Rcpp, Rhdf5lib Suggests: BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix, BiocStyle, testthat, rmarkdown, knitr License: GPL-3 Archs: x64 Package: chimeraviz Version: 1.30.0 Depends: Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors, ensembldb, AnnotationFilter, data.table Imports: methods, grid, Rsamtools, GenomeInfoDb, GenomicAlignments, RColorBrewer, graphics, AnnotationDbi, RCircos, org.Hs.eg.db, org.Mm.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr, dplyr, BiocStyle, checkmate, gtools, magick Suggests: testthat, roxygen2, devtools, knitr, lintr License: Artistic-2.0 Package: ChIPanalyser Version: 1.26.0 Depends: R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel Imports: methods, IRanges, S4Vectors,grDevices,graphics,stats,utils,rtracklayer,ROCR, BiocManager,GenomeInfoDb,RColorBrewer Suggests: BSgenome.Dmelanogaster.UCSC.dm6,knitr, RUnit, BiocGenerics License: GPL-3 Package: ChIPComp Version: 1.34.0 Depends: R (>= 3.2.0),GenomicRanges,IRanges,rtracklayer,GenomeInfoDb,S4Vectors Imports: Rsamtools,limma,BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9,BiocGenerics Suggests: BiocStyle,RUnit License: GPL Archs: x64 Package: chipenrich Version: 2.28.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, BiocGenerics, chipenrich.data, GenomeInfoDb, GenomicRanges, grDevices, grid, IRanges, lattice, latticeExtra, MASS, methods, mgcv, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, parallel, plyr, rms, rtracklayer, S4Vectors (>= 0.23.10), stats, stringr, utils Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat License: GPL-3 Package: ChIPexoQual Version: 1.28.0 Depends: R (>= 3.5.0), GenomicAlignments (>= 1.0.1) Imports: methods, utils, GenomeInfoDb, stats, BiocParallel, GenomicRanges (>= 1.14.4), ggplot2 (>= 1.0), data.table (>= 1.9.6), Rsamtools (>= 1.16.1), IRanges (>= 1.6), S4Vectors (>= 0.8), biovizBase (>= 1.18), broom (>= 0.4), RColorBrewer (>= 1.1), dplyr (>= 0.5), scales (>= 0.4.0), viridis (>= 0.3), hexbin (>= 1.27), rmarkdown Suggests: ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat License: GPL (>= 2) Package: ChIPpeakAnno Version: 3.38.1 Depends: R (>= 3.5), methods, IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), S4Vectors (>= 0.17.25) Imports: AnnotationDbi, BiocGenerics (>= 0.1.0), Biostrings (>= 2.47.6), pwalign, DBI, dplyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, RBGL, Rsamtools, SummarizedExperiment, VennDiagram, biomaRt, ggplot2, grDevices, graph, graphics, grid, InteractionSet, KEGGREST, matrixStats, multtest, regioneR, rtracklayer, stats, utils, universalmotif, stringr, tibble, tidyr, data.table, scales, ensembldb Suggests: AnnotationHub, BSgenome, limma, reactome.db, BiocManager, BiocStyle, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg38, DelayedArray, idr, seqinr, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, EnsDb.Hsapiens.v86, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR, knitr, rmarkdown, reshape2, testthat, trackViewer, motifStack, OrganismDbi, BiocFileCache License: GPL (>= 2) Package: ChIPQC Version: 1.40.0 Depends: R (>= 3.5.0), ggplot2, DiffBind, GenomicRanges (>= 1.17.19), BiocParallel Imports: BiocGenerics (>= 0.11.3), S4Vectors (>= 0.1.0), IRanges (>= 1.99.17), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), chipseq (>= 1.12.0), gtools, methods, reshape2, Nozzle.R1, Biobase, grDevices, stats, utils, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene Suggests: BiocStyle License: GPL (>= 3) Package: ChIPseeker Version: 1.40.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, BiocGenerics, boot, enrichplot, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, graphics, grDevices, gtools, methods, plotrix, dplyr, parallel, magrittr, rtracklayer, S4Vectors, stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, aplot, yulab.utils, tibble Suggests: clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram, ReactomePA, org.Hs.eg.db, knitr, rmarkdown, testthat, prettydoc License: Artistic-2.0 Package: chipseq Version: 1.54.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), ShortRead Imports: methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges, ShortRead Suggests: BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr License: Artistic-2.0 Archs: x64 Package: ChIPseqR Version: 1.58.0 Depends: R (>= 2.10.0), methods, BiocGenerics, S4Vectors (>= 0.9.25) Imports: Biostrings, fBasics, GenomicRanges, IRanges (>= 2.5.14), graphics, grDevices, HilbertVis, ShortRead, stats, timsac, utils License: GPL (>= 2) Archs: x64 Package: ChIPsim Version: 1.58.0 Depends: Biostrings (>= 2.29.2) Imports: IRanges, XVector, Biostrings, ShortRead, graphics, methods, stats, utils Suggests: actuar, zoo License: GPL (>= 2) Package: chopsticks Version: 1.70.0 Imports: graphics, stats, utils, methods, survival Suggests: hexbin License: GPL-3 Archs: x64 Package: chromDraw Version: 2.34.0 Depends: R (>= 3.0.0) Imports: Rcpp (>= 0.11.1), GenomicRanges (>= 1.17.46) LinkingTo: Rcpp License: GPL-3 Archs: x64 Package: ChromHeatMap Version: 1.58.0 Depends: R (>= 2.9.0), BiocGenerics (>= 0.3.2), annotate (>= 1.20.0), AnnotationDbi (>= 1.4.0) Imports: Biobase (>= 2.17.8), graphics, grDevices, methods, stats, IRanges, rtracklayer, GenomicRanges Suggests: ALL, hgu95av2.db License: Artistic-2.0 Package: chromPlot Version: 1.32.0 Depends: stats, utils, graphics, grDevices, datasets, base, biomaRt, GenomicRanges, R (>= 3.1.0) Suggests: qtl, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) Package: ChromSCape Version: 1.14.0 Depends: R (>= 4.1) Imports: shiny, colourpicker, shinyjs, rtracklayer, shinyFiles, shinyhelper, shinyWidgets, shinydashboardPlus, shinycssloaders, Matrix, plotly, shinydashboard, colorRamps, kableExtra, viridis, batchelor, BiocParallel, parallel, Rsamtools, ggplot2, ggrepel, gggenes, gridExtra, qualV, stringdist, stringr, fs, qs, DT, scran, scater, ConsensusClusterPlus, Rtsne, dplyr, tidyr, GenomicRanges, IRanges, irlba, rlist, umap, tibble, methods, jsonlite, edgeR, stats, graphics, grDevices, utils, S4Vectors, SingleCellExperiment, SummarizedExperiment, msigdbr, forcats, Rcpp, coop, matrixTests, DelayedArray LinkingTo: Rcpp Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, Signac, future, igraph, bluster, httr License: GPL-3 Archs: x64 Package: chromstaR Version: 1.30.0 Depends: R (>= 3.5.0), GenomicRanges, ggplot2, chromstaRData Imports: methods, utils, grDevices, graphics, stats, foreach, doParallel, BiocGenerics (>= 0.31.6), S4Vectors, GenomeInfoDb, IRanges, reshape2, Rsamtools, GenomicAlignments, bamsignals, mvtnorm Suggests: knitr, BiocStyle, testthat, biomaRt License: Artistic-2.0 Archs: x64 Package: chromVAR Version: 1.26.0 Depends: R (>= 3.5.0) Imports: IRanges, GenomeInfoDb, GenomicRanges, ggplot2, nabor, BiocParallel, BiocGenerics, Biostrings, TFBSTools, Rsamtools, S4Vectors, methods, Rcpp, grid, plotly, shiny, miniUI, stats, utils, graphics, DT, Rtsne, Matrix, SummarizedExperiment, RColorBrewer, BSgenome LinkingTo: Rcpp, RcppArmadillo Suggests: JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr License: MIT + file LICENSE Archs: x64 Package: CHRONOS Version: 1.32.0 Depends: R (>= 3.5) Imports: XML, RCurl, RBGL, parallel, foreach, doParallel, openxlsx, igraph, circlize, graph, stats, utils, grDevices, graphics, methods, biomaRt, rJava Suggests: RUnit, BiocGenerics, knitr, rmarkdown License: GPL-2 Package: cicero Version: 1.22.0 Depends: R (>= 3.5.0), monocle, Gviz (>= 1.22.3) Imports: assertthat (>= 0.2.0), Biobase (>= 2.37.2), BiocGenerics (>= 0.23.0), data.table (>= 1.10.4), dplyr (>= 0.7.4), FNN (>= 1.1), GenomicRanges (>= 1.30.3), ggplot2 (>= 2.2.1), glasso (>= 1.8), grDevices, igraph (>= 1.1.0), IRanges (>= 2.10.5), Matrix (>= 1.2-12), methods, parallel, plyr (>= 1.8.4), reshape2 (>= 1.4.3), S4Vectors (>= 0.14.7), stats, stringi, stringr (>= 1.2.0), tibble (>= 1.4.2), tidyr, VGAM (>= 1.0-5), utils Suggests: AnnotationDbi (>= 1.38.2), knitr, markdown, rmarkdown, rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr License: MIT + file LICENSE Package: CIMICE Version: 1.12.0 Imports: dplyr, ggplot2, glue, tidyr, igraph, networkD3, visNetwork, ggcorrplot, purrr, ggraph, stats, utils, maftools, assertthat, tidygraph, expm, Matrix Suggests: BiocStyle, knitr, rmarkdown, testthat, webshot License: Artistic-2.0 Package: CINdex Version: 1.32.0 Depends: R (>= 3.3), GenomicRanges Imports: bitops,gplots,grDevices,som, dplyr,gridExtra,png,stringr,S4Vectors, IRanges, GenomeInfoDb,graphics, stats, utils Suggests: knitr, testthat, ReactomePA, RUnit, BiocGenerics, AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings,Homo.sapiens, R.utils License: GPL (>= 2) Package: circRNAprofiler Version: 1.18.0 Depends: R(>= 4.3.0) Imports: dplyr, magrittr, readr, rtracklayer, stringr, stringi, DESeq2, edgeR, GenomicRanges, IRanges, seqinr, R.utils, reshape2, ggplot2, utils, rlang, S4Vectors, stats, GenomeInfoDb, universalmotif, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, Biostrings, gwascat, BSgenome, Suggests: testthat, knitr, roxygen2, rmarkdown, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocManager, License: GPL-3 Package: cisPath Version: 1.44.0 Depends: R (>= 2.10.0) Imports: methods, utils License: GPL (>= 3) Archs: x64 Package: CiteFuse Version: 1.16.0 Depends: R (>= 4.0) Imports: SingleCellExperiment (>= 1.8.0), SummarizedExperiment (>= 1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid, dbscan, uwot, Rtsne, S4Vectors (>= 0.24.0), igraph, scales, scran (>= 1.14.6), graphics, methods, stats, utils, reshape2, ggridges, randomForest, pheatmap, ggraph, grDevices, rhdf5, rlang, Rcpp, compositions LinkingTo: Rcpp Suggests: knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle, pkgdown License: GPL-3 Archs: x64 Package: ClassifyR Version: 3.8.2 Depends: R (>= 4.1.0), generics, methods, S4Vectors, MultiAssayExperiment, BiocParallel, survival Imports: grid, genefilter, utils, dplyr, tidyr, rlang, ranger, ggplot2 (>= 3.0.0), ggpubr, reshape2, ggupset Suggests: limma, edgeR, car, Rmixmod, gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, parathyroidSE, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, robustbase, glmnet, class, randomForestSRC, MatrixModels, xgboost, data.tree, ggnewscale License: GPL-3 Archs: x64 Package: cleanUpdTSeq Version: 1.42.0 Depends: R (>= 3.5.0), BSgenome.Drerio.UCSC.danRer7, methods Imports: BSgenome, GenomicRanges, seqinr, e1071, Biostrings, GenomeInfoDb, IRanges, utils, stringr, stats, S4Vectors Suggests: BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics (>= 0.1.0) License: GPL-2 Package: cleaver Version: 1.42.0 Depends: R (>= 3.0.0), methods, Biostrings (>= 1.29.8) Imports: S4Vectors, IRanges Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown, BRAIN, UniProt.ws (>= 2.36.5) License: GPL (>= 3) Package: clevRvis Version: 1.4.0 Imports: shiny, ggraph, igraph, ggiraph, cowplot, htmlwidgets, readxl, dplyr, readr, purrr, tibble, patchwork, R.utils, shinyWidgets, colorspace, shinyhelper, shinycssloaders, ggnewscale, shinydashboard, DT, colourpicker, grDevices, methods, utils, stats, ggplot2, magrittr, tools Suggests: knitr, rmarkdown, BiocStyle License: LGPL-3 Package: clippda Version: 1.54.0 Depends: R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d, graphics, grDevices, stats, utils, Biobase, tools, methods License: GPL (>= 2) Package: clipper Version: 1.44.0 Depends: R (>= 2.15.0), Matrix, graph Imports: methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph, KEGGgraph, corpcor Suggests: RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS, BiocStyle Enhances: RCy3 License: AGPL-3 Package: cliProfiler Version: 1.10.0 Depends: S4Vectors, methods, R (>= 4.1) Imports: dplyr, rtracklayer, GenomicRanges, ggplot2, BSgenome, Biostrings, utils Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 Package: Clomial Version: 1.40.0 Depends: R (>= 2.10), matrixStats Imports: methods, permute License: GPL (>= 2) Package: clst Version: 1.52.0 Depends: R (>= 2.10) Imports: ROC, lattice Suggests: RUnit License: GPL-3 Package: clstutils Version: 1.52.0 Depends: R (>= 2.10), clst, rjson, ape Imports: lattice, RSQLite Suggests: RUnit License: GPL-3 Package: CluMSID Version: 1.20.0 Depends: R (>= 3.6) Imports: mzR, S4Vectors, dbscan, RColorBrewer, ape, network, GGally, ggplot2, plotly, methods, utils, stats, sna, grDevices, graphics, Biobase, gplots, MSnbase Suggests: knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr, CluMSIDdata, metaMS, metaMSdata, xcms License: MIT + file LICENSE Package: ClustAll Version: 1.0.0 Depends: R (>= 4.2.0) Imports: FactoMineR, bigstatsr, clValid, doSNOW, parallel, foreach, dplyr, fpc, mice, modeest, flock, networkD3, methods, ComplexHeatmap, cluster, RColorBrewer, circlize, grDevices, ggplot2, grid, stats, utils, pbapply Suggests: RUnit, knitr, BiocGenerics, rmarkdown, BiocStyle, roxygen2 License: GPL-2 Package: clustComp Version: 1.32.0 Depends: R (>= 3.3) Imports: sm, stats, graphics, grDevices Suggests: Biobase, colonCA, RUnit, BiocGenerics License: GPL (>= 2) Package: clusterExperiment Version: 2.24.0 Depends: R (>= 3.6.0), SingleCellExperiment, SummarizedExperiment (>= 1.15.4), BiocGenerics Imports: methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats, limma, locfdr, matrixStats, graphics, parallel, BiocSingular, kernlab, stringr, S4Vectors, grDevices, DelayedArray (>= 0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp, edgeR, scales, zinbwave, phylobase, pracma, mbkmeans LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph, rmarkdown License: Artistic-2.0 Archs: x64 Package: ClusterFoldSimilarity Version: 1.0.0 Imports: methods, igraph, ggplot2, scales, BiocParallel, graphics, stats, utils, Matrix, cowplot, dplyr, reshape2, Seurat, SeuratObject, SingleCellExperiment, ggdendro Suggests: knitr, rmarkdown, kableExtra, scRNAseq, BiocStyle License: Artistic-2.0 Package: ClusterJudge Version: 1.26.0 Depends: R (>= 3.6), stats, utils, graphics, infotheo, lattice, latticeExtra, httr, jsonlite Suggests: yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt License: Artistic-2.0 Package: clusterProfiler Version: 4.12.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, downloader, DOSE (>= 3.23.2), dplyr, enrichplot (>= 1.9.3), GO.db, GOSemSim (>= 2.27.2), gson (>= 0.0.7), httr, igraph, magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils, yulab.utils (>= 0.0.7) Suggests: AnnotationHub, knitr, jsonlite, readr, rmarkdown, org.Hs.eg.db, prettydoc, BiocManager, testthat License: Artistic-2.0 Package: clusterSeq Version: 1.28.0 Depends: R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats, utils Imports: BiocGenerics Suggests: BiocStyle License: GPL-3 Package: ClusterSignificance Version: 1.32.0 Depends: R (>= 3.3.0) Imports: methods, pracma, princurve (>= 2.0.5), scatterplot3d, RColorBrewer, grDevices, graphics, utils, stats Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr License: GPL-3 Package: clusterStab Version: 1.76.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 Package: clustifyr Version: 1.16.0 Depends: R (>= 2.10) Imports: cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, rlang, scales, stringr, tibble, tidyr, stats, methods, SingleCellExperiment, SummarizedExperiment, SeuratObject, matrixStats, S4Vectors, proxy, httr, utils Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, gprofiler2, purrr, data.table, R.utils License: MIT + file LICENSE Package: ClustIRR Version: 1.2.0 Depends: R (>= 4.3.0) Imports: stringdist, methods, stats, utils, igraph, visNetwork, blaster, pwalign, grDevices, parallel Suggests: BiocStyle, knitr, testthat, ggplot2, patchwork, ggrepel License: GPL-3 + file LICENSE Package: CMA Version: 1.62.0 Depends: R (>= 2.10), methods, stats, Biobase Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm License: GPL (>= 2) Package: cmapR Version: 1.16.0 Depends: R (>= 4.0) Imports: methods, rhdf5, data.table, flowCore, SummarizedExperiment, matrixStats Suggests: knitr, testthat, BiocStyle, rmarkdown License: file LICENSE Package: CNAnorm Version: 1.50.0 Depends: R (>= 2.10.1), methods Imports: DNAcopy License: GPL-2 Archs: x64 Package: CNEr Version: 1.40.0 Depends: R (>= 3.5.0) Imports: Biostrings (>= 2.33.4), pwalign, DBI (>= 0.7), RSQLite (>= 0.11.4), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.23.16), rtracklayer (>= 1.25.5), XVector (>= 0.5.4), GenomicAlignments (>= 1.1.9), methods, S4Vectors (>= 0.13.13), IRanges (>= 2.5.27), readr (>= 0.2.2), BiocGenerics, tools, parallel, reshape2 (>= 1.4.1), ggplot2 (>= 2.1.0), poweRlaw (>= 0.60.3), annotate (>= 1.50.0), GO.db (>= 3.3.0), R.utils (>= 2.3.0), KEGGREST (>= 1.14.0) LinkingTo: S4Vectors, IRanges, XVector Suggests: Gviz (>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Ggallus.UCSC.galGal3 License: GPL-2 | file LICENSE License_restricts_use: yes Archs: x64 Package: cn.farms Version: 1.52.0 Depends: R (>= 3.0), Biobase, methods, ff, oligoClasses, snow Imports: DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, pd.genomewidesnp.6 License: LGPL (>= 2.0) Archs: x64 Package: cn.mops Version: 1.50.0 Depends: R (>= 3.5.0), methods, utils, stats, graphics, parallel, GenomicRanges Imports: BiocGenerics, Biobase, IRanges, Rsamtools, GenomeInfoDb, S4Vectors Suggests: DNAcopy License: LGPL (>= 2.0) Archs: x64 Package: CNORdt Version: 1.46.0 Depends: R (>= 1.8.0), CellNOptR (>= 0.99), abind License: GPL-2 Archs: x64 Package: CNORfeeder Version: 1.44.0 Depends: R (>= 3.6.0), CellNOptR (>= 1.4.0), graph Suggests: minet, Rgraphviz, RUnit, BiocGenerics, igraph Enhances: MEIGOR License: GPL-3 Package: CNORfuzzy Version: 1.46.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), nloptr (>= 0.8.5) Suggests: xtable, Rgraphviz, RUnit, BiocGenerics License: GPL-2 Archs: x64 Package: CNORode Version: 1.46.0 Depends: CellNOptR, genalg Suggests: knitr, rmarkdown Enhances: doParallel, foreach License: GPL-2 Archs: x64 Package: CNTools Version: 1.60.0 Depends: R (>= 2.10), methods, tools, stats, genefilter License: LGPL Archs: x64 Package: CNVfilteR Version: 1.18.0 Depends: R (>= 4.3) Imports: IRanges, GenomicRanges, SummarizedExperiment, pracma, regioneR, assertthat, karyoploteR, CopyNumberPlots, graphics, utils, VariantAnnotation, Rsamtools, GenomeInfoDb, Biostrings, methods Suggests: knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown License: Artistic-2.0 Package: CNVgears Version: 1.12.0 Depends: R (>= 4.1), data.table Imports: ggplot2 Suggests: VariantAnnotation, DelayedArray, knitr, biomaRt, evobiR, rmarkdown, devtools, cowplot, usethis, scales, testthat, GenomicRanges, cn.mops, R.utils License: GPL-3 Package: cnvGSA Version: 1.48.0 Depends: brglm, doParallel, foreach, GenomicRanges, methods, splitstackshape Suggests: cnvGSAdata, org.Hs.eg.db License: LGPL Package: CNViz Version: 1.12.0 Depends: R (>= 4.0), shiny (>= 1.5.0) Imports: dplyr, stats, utils, grDevices, plotly, karyoploteR, CopyNumberPlots, GenomicRanges, magrittr, DT, scales, graphics Suggests: rmarkdown, knitr License: Artistic-2.0 Package: CNVMetrics Version: 1.8.0 Depends: R (>= 4.0) Imports: GenomicRanges, IRanges, S4Vectors, BiocParallel, methods, magrittr, stats, pheatmap, gridExtra, grDevices, rBeta2009 Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 Package: CNVPanelizer Version: 1.36.0 Depends: R (>= 3.2.0), GenomicRanges Imports: BiocGenerics, S4Vectors, grDevices, stats, utils, NOISeq, IRanges, Rsamtools, foreach, ggplot2, plyr, GenomeInfoDb, gplots, reshape2, stringr, testthat, graphics, methods, shiny, shinyFiles, shinyjs, grid, openxlsx Suggests: knitr, RUnit License: GPL-3 Package: CNVRanger Version: 1.20.0 Depends: GenomicRanges, RaggedExperiment Imports: BiocGenerics, BiocParallel, GDSArray, GenomeInfoDb, IRanges, S4Vectors, SNPRelate, SummarizedExperiment, data.table, edgeR, gdsfmt, grDevices, lattice, limma, methods, plyr, qqman, rappdirs, reshape2, stats, utils Suggests: AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment, TCGAutils, TxDb.Hsapiens.UCSC.hg19.knownGene, curatedTCGAData, ensembldb, grid, knitr, org.Hs.eg.db, regioneR, rmarkdown, statmod License: Artistic-2.0 Package: CNVrd2 Version: 1.42.0 Depends: R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags, ggplot2, gridExtra Imports: DNAcopy, IRanges, Rsamtools Suggests: knitr License: GPL-2 Package: CoCiteStats Version: 1.76.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL Package: COCOA Version: 2.18.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocGenerics, S4Vectors, IRanges, data.table, ggplot2, Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid, grDevices, simpleCache, fitdistrplus Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 Package: codelink Version: 1.72.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>= 2.17.8), limma Imports: annotate Suggests: genefilter, parallel, knitr License: GPL-2 Package: CODEX Version: 1.36.0 Depends: R (>= 3.2.3), Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors Suggests: WES.1KG.WUGSC License: GPL-2 Package: CoGAPS Version: 3.24.0 Depends: R (>= 3.5.0) Imports: BiocParallel, cluster, methods, gplots, graphics, grDevices, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tools, utils, rhdf5, dplyr, fgsea, forcats, ggplot2 LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, BiocStyle, SeuratObject, BiocFileCache License: BSD_3_clause + file LICENSE Archs: x64 Package: cogena Version: 1.38.0 Depends: R (>= 3.6), cluster, ggplot2, kohonen Imports: methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, stringr, tibble, tidyr, dplyr, devtools Suggests: knitr, rmarkdown (>= 2.1) License: LGPL-3 Package: cogeqc Version: 1.8.0 Depends: R (>= 4.2.0) Imports: utils, graphics, stats, methods, reshape2, ggplot2, scales, ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite, Biostrings Suggests: testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle, rmarkdown, covr License: GPL-3 Package: Cogito Version: 1.10.0 Depends: R (>= 4.1), GenomicRanges, jsonlite, GenomicFeatures, entropy Imports: BiocManager, rmarkdown, GenomeInfoDb, S4Vectors, AnnotationDbi, graphics, stats, utils, methods, magrittr, ggplot2, TxDb.Mmusculus.UCSC.mm9.knownGene Suggests: BiocStyle, knitr, markdown, testthat (>= 3.0.0) License: LGPL-3 Package: coGPS Version: 1.48.0 Depends: R (>= 2.13.0) Imports: graphics, grDevices Suggests: limma License: GPL-2 Package: cola Version: 2.10.0 Depends: R (>= 4.0.0) Imports: grDevices, graphics, grid, stats, utils, ComplexHeatmap (>= 2.5.4), matrixStats, GetoptLong, circlize (>= 0.4.7), GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer, cluster, skmeans, png, mclust, crayon, methods, xml2, microbenchmark, httr, knitr (>= 1.4.0), markdown (>= 1.6), digest, impute, brew, Rcpp (>= 0.11.0), BiocGenerics, eulerr, foreach, doParallel, doRNG, irlba LinkingTo: Rcpp Suggests: genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE, AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree, dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot, flexclust, randomForest, e1071 License: MIT + file LICENSE Archs: x64 Package: comapr Version: 1.8.0 Depends: R (>= 4.1.0) Imports: methods, ggplot2, reshape2, dplyr, gridExtra, plotly, circlize, rlang, GenomicRanges, IRanges, foreach, BiocParallel, GenomeInfoDb, scales, RColorBrewer, tidyr, S4Vectors, utils, Matrix, grid, stats, SummarizedExperiment, plyr, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod License: MIT + file LICENSE Package: combi Version: 1.16.0 Depends: R (>= 4.0), DBI Imports: ggplot2, nleqslv, phyloseq, tensor, stats, limma, Matrix (>= 1.6.0), BB, reshape2, alabama, cobs, Biobase, vegan, grDevices, graphics, methods, SummarizedExperiment Suggests: knitr, rmarkdown, testthat License: GPL-2 Package: coMethDMR Version: 1.8.0 Depends: R (>= 4.1) Imports: AnnotationHub, BiocParallel, bumphunter, ExperimentHub, GenomicRanges, IRanges, lmerTest, methods, stats, utils Suggests: BiocStyle, corrplot, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: GPL-3 Package: compartmap Version: 1.22.0 Depends: R (>= 4.1.0), SummarizedExperiment, RaggedExperiment, BiocSingular, HDF5Array Imports: GenomicRanges, parallel, grid, ggplot2, reshape2, scales, DelayedArray, rtracklayer, DelayedMatrixStats, Matrix, RMTstat Suggests: covr, testthat, knitr, Rcpp, rmarkdown, markdown License: GPL-3 + file LICENSE Package: COMPASS Version: 1.42.0 Depends: R (>= 3.0.3) Imports: methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr, knitr, abind, clue, grDevices, utils, pdist, magrittr, reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown, foreach, coda LinkingTo: Rcpp (>= 0.11.0) Suggests: flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2, progress License: Artistic-2.0 Archs: x64 Package: compcodeR Version: 1.40.0 Depends: R (>= 4.0), sm Imports: knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots, gtools, caTools, grid, KernSmooth, MASS, ggplot2, stringr, modeest, edgeR, limma, vioplot, methods, stats, utils, ape, phylolm, matrixStats, grDevices, graphics, rmarkdown, shiny, shinydashboard Suggests: BiocStyle, EBSeq, DESeq2 (>= 1.1.31), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva, tcltk Enhances: rpanel, DSS License: GPL (>= 2) Package: compEpiTools Version: 1.38.0 Depends: R (>= 3.5.0), methods, topGO, GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel, grDevices, gplots, IRanges, GenomicFeatures, XVector, methylPipe, GO.db, S4Vectors, GenomeInfoDb Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer License: GPL Package: ComplexHeatmap Version: 2.20.0 Depends: R (>= 3.5.0), methods, grid, graphics, stats, grDevices Imports: circlize (>= 0.4.14), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges, matrixStats, foreach, doParallel, codetools Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff, fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12), gridGraphics, gplots, rmarkdown, Cairo, magick License: MIT + file LICENSE Package: CompoundDb Version: 1.8.0 Depends: R (>= 4.1), methods, AnnotationFilter, S4Vectors Imports: BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr, RSQLite, Biobase, ProtGenerics (>= 1.35.3), xml2, IRanges, Spectra (>= 1.9.12), MsCoreUtils, MetaboCoreUtils, BiocParallel Suggests: knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19), MsBackendMgf License: Artistic-2.0 Package: ComPrAn Version: 1.12.0 Imports: data.table, dplyr, forcats, ggplot2, magrittr, purrr, tidyr, rlang, stringr, shiny, DT, RColorBrewer, VennDiagram, rio, scales, shinydashboard, shinyjs, stats, tibble, grid Suggests: testthat (>= 2.1.0), knitr, rmarkdown License: MIT + file LICENSE Package: compSPOT Version: 1.2.0 Depends: R (>= 4.3.0) Imports: stats, base, ggplot2, plotly, magrittr, ggpubr, gridExtra, utils, data.table Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 Package: concordexR Version: 1.4.0 Depends: R (>= 4.2) Imports: BiocParallel, cli, DelayedArray, ggplot2, Matrix, methods, pheatmap, rlang, scales Suggests: BiocNeighbors, BiocStyle, bluster, covr, knitr, patchwork, rmarkdown, scater, TENxPBMCData, testthat (>= 3.0.0), vdiffr License: Artistic-2.0 Package: condiments Version: 1.12.0 Depends: R (>= 4.0) Imports: slingshot (>= 1.9), mgcv, RANN, stats, SingleCellExperiment, SummarizedExperiment, utils, magrittr, dplyr (>= 1.0), Ecume (>= 0.9.1), methods, pbapply, matrixStats, BiocParallel, TrajectoryUtils, igraph, distinct Suggests: knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN License: MIT + file LICENSE Package: CONFESS Version: 1.32.0 Depends: R (>= 3.3),grDevices,utils,stats,graphics Imports: methods,changepoint,cluster,contrast,data.table(>= 1.9.7),ecp,EBImage,flexmix,flowCore,flowClust,flowMeans,flowMerge,flowPeaks,foreach,ggplot2,grid,limma,MASS,moments,outliers,parallel,plotrix,raster,readbitmap,reshape2,SamSPECTRAL,waveslim,wavethresh,zoo Suggests: BiocStyle, knitr, rmarkdown, CONFESSdata License: GPL-2 Package: consensus Version: 1.22.0 Depends: R (>= 3.5), RColorBrewer Imports: matrixStats, gplots, grDevices, methods, graphics, stats, utils Suggests: knitr, RUnit, rmarkdown, BiocGenerics License: BSD_3_clause + file LICENSE Package: ConsensusClusterPlus Version: 1.68.0 Imports: Biobase, ALL, graphics, stats, utils, cluster License: GPL-2 Package: consensusDE Version: 1.22.0 Depends: R (>= 3.5), BiocGenerics Imports: airway, AnnotationDbi, BiocParallel, Biobase, Biostrings, data.table, dendextend, DESeq2 (>= 1.20.0), EDASeq, ensembldb, edgeR, EnsDb.Hsapiens.v86, GenomicAlignments, GenomicFeatures, limma, org.Hs.eg.db, pcaMethods, RColorBrewer, Rsamtools, RUVSeq, S4Vectors, stats, SummarizedExperiment, TxDb.Dmelanogaster.UCSC.dm3.ensGene, utils Suggests: knitr, rmarkdown License: GPL-3 Package: consensusOV Version: 1.26.0 Depends: R (>= 3.6) Imports: Biobase, GSVA (>= 1.50.0), gdata, genefu, limma, matrixStats, randomForest, stats, utils, methods, BiocParallel Suggests: BiocStyle, ggplot2, knitr, rmarkdown, magick License: Artistic-2.0 Package: consensusSeekeR Version: 1.32.0 Depends: R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges, BiocParallel Imports: GenomeInfoDb, rtracklayer, stringr, S4Vectors, methods Suggests: BiocStyle, ggplot2, knitr, rmarkdown, RUnit License: Artistic-2.0 Package: consICA Version: 2.2.0 Depends: R (>= 4.2.0) Imports: fastICA (>= 1.2.1), sm, org.Hs.eg.db, GO.db, stats, SummarizedExperiment, BiocParallel, graph, ggplot2, methods, Rfast, pheatmap, survival, topGO, graphics, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat, Seurat License: MIT + file LICENSE Package: CONSTANd Version: 1.12.0 Depends: R (>= 4.1) Suggests: BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra, magick, Cairo, limma License: file LICENSE Package: convert Version: 1.80.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray, utils, methods License: LGPL Package: copa Version: 1.72.0 Depends: Biobase, methods Suggests: colonCA License: Artistic-2.0 Archs: x64 Package: CopyNumberPlots Version: 1.20.0 Depends: R (>= 3.6), karyoploteR Imports: regioneR, IRanges, Rsamtools, SummarizedExperiment, VariantAnnotation, methods, stats, GenomeInfoDb, GenomicRanges, cn.mops, rhdf5, utils Suggests: BiocStyle, knitr, rmarkdown, panelcn.mops, BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy, testthat License: Artistic-2.0 Package: coRdon Version: 1.22.0 Depends: R (>= 3.5) Imports: methods, stats, utils, Biostrings, Biobase, dplyr, stringr, purrr, ggplot2, data.table Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 Package: CoRegNet Version: 1.42.0 Depends: R (>= 2.14), igraph, shiny, arules, methods Suggests: RColorBrewer, gplots, BiocStyle, knitr, rmarkdown License: GPL-3 Archs: x64 Package: CoreGx Version: 2.8.0 Depends: R (>= 4.1), BiocGenerics, SummarizedExperiment Imports: Biobase, S4Vectors, MultiAssayExperiment, MatrixGenerics, piano, BiocParallel, parallel, BumpyMatrix, checkmate, methods, stats, utils, graphics, grDevices, lsa, data.table, crayon, glue, rlang, bench Suggests: pander, markdown, BiocStyle, rmarkdown, knitr, formatR, testthat License: GPL (>= 3) Package: Cormotif Version: 1.50.0 Depends: R (>= 2.12.0), affy, limma Imports: affy, graphics, grDevices License: GPL-2 Package: corral Version: 1.14.0 Imports: ggplot2, ggthemes, grDevices, gridExtra, irlba, Matrix, methods, MultiAssayExperiment, pals, reshape2, SingleCellExperiment, SummarizedExperiment, transport Suggests: ade4, BiocStyle, CellBench, DuoClustering2018, knitr, rmarkdown, scater, testthat License: GPL-2 Package: coseq Version: 1.28.0 Depends: R (>= 4.0.0), SummarizedExperiment, S4Vectors Imports: edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2, scales, HTSFilter, corrplot, HTSCluster, grDevices, graphics, stats, methods, compositions, mvtnorm Suggests: Biobase, knitr, rmarkdown, testthat, BiocStyle License: GPL-3 Package: cosmiq Version: 1.38.0 Depends: R (>= 3.6), Rcpp Imports: pracma, xcms, MassSpecWavelet, faahKO Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 Archs: x64 Package: cosmosR Version: 1.12.0 Depends: R (>= 4.1) Imports: CARNIVAL, dorothea, dplyr, GSEABase, igraph, progress, purrr, rlang, stringr, utils, visNetwork, decoupleR Suggests: testthat, knitr, rmarkdown, piano, ggplot2 License: GPL-3 Package: COSNet Version: 1.38.0 Suggests: bionetdata, PerfMeas, RUnit, BiocGenerics License: GPL (>= 2) Archs: x64 Package: COTAN Version: 2.4.4 Depends: R (>= 4.2) Imports: stats, plyr, dplyr, methods, grDevices, Matrix, ggplot2, ggrepel, ggthemes, graphics, parallel, parallelly, tibble, tidyr, BiocSingular, PCAtools, parallelDist, ComplexHeatmap, circlize, grid, scales, RColorBrewer, utils, rlang, Rfast, stringr, Seurat, umap, dendextend, zeallot, assertthat, withr Suggests: testthat (>= 3.0.0), proto, spelling, knitr, data.table, gsubfn, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS, Rtsne, plotly, BiocStyle, cowplot, qpdf, GEOquery, sf, torch License: GPL-3 Package: countsimQC Version: 1.22.0 Depends: R (>= 3.5) Imports: rmarkdown (>= 2.5), edgeR, DESeq2 (>= 1.16.0), dplyr, tidyr, ggplot2, grDevices, tools, SummarizedExperiment, genefilter, DT, GenomeInfoDbData, caTools, randtests, stats, utils, methods, ragg Suggests: knitr, testthat License: GPL (>= 2) Package: covEB Version: 1.30.0 Depends: R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats, LaplacesDemon, Matrix Suggests: curatedBladderData License: GPL-3 Package: covRNA Version: 1.30.0 Depends: ade4, Biobase Imports: parallel, genefilter, grDevices, stats, graphics Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) Package: cpvSNP Version: 1.36.0 Depends: R (>= 3.5.0), GenomicFeatures, GSEABase (>= 1.24.0) Imports: methods, corpcor, BiocParallel, ggplot2, plyr Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle License: Artistic-2.0 Package: cqn Version: 1.50.0 Depends: R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore, splines, quantreg Imports: splines Suggests: scales, edgeR License: Artistic-2.0 Package: CRImage Version: 1.52.0 Depends: EBImage, DNAcopy, aCGH Imports: MASS, e1071, foreach, sgeostat License: Artistic-2.0 Package: CRISPRball Version: 1.0.0 Depends: R (>= 4.4.0), shinyBS Imports: DT, shiny, grid, ComplexHeatmap, InteractiveComplexHeatmap, graphics, stats, ggplot2, plotly, shinyWidgets, shinycssloaders, shinyjqui, dittoSeq, matrixStats, colourpicker, shinyjs, MAGeCKFlute, circlize, PCAtools, utils, grDevices, htmlwidgets, methods Suggests: BiocStyle, msigdbr, depmap, pool, RSQLite, mygene, testthat (>= 3.0.0), knitr, rmarkdown License: MIT + file LICENSE Package: crisprBase Version: 1.8.0 Depends: utils, methods, R (>= 4.1) Imports: BiocGenerics, Biostrings, GenomicRanges, graphics, IRanges, S4Vectors, stringr Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE Package: crisprBowtie Version: 1.8.0 Depends: methods Imports: BiocGenerics, Biostrings, BSgenome, crisprBase (>= 0.99.15), GenomeInfoDb, GenomicRanges, IRanges, Rbowtie, readr, stats, stringr, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat License: MIT + file LICENSE Package: crisprDesign Version: 1.6.0 Depends: R (>= 4.2.0), crisprBase (>= 1.1.3) Imports: AnnotationDbi, BiocGenerics, Biostrings, BSgenome, crisprBowtie (>= 0.99.8), crisprScore (>= 1.1.6), GenomeInfoDb, GenomicFeatures, GenomicRanges (>= 1.38.0), IRanges, Matrix, MatrixGenerics, methods, rtracklayer, S4Vectors, stats, txdbmaker, utils, VariantAnnotation Suggests: biomaRt, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa (>= 0.99.7), knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat License: MIT + file LICENSE Package: crisprScore Version: 1.8.0 Depends: R (>= 4.1), crisprScoreData (>= 1.1.3) Imports: basilisk (>= 1.9.2), basilisk.utils (>= 1.9.1), BiocGenerics, Biostrings, IRanges, methods, randomForest, reticulate, stringr, utils, XVector Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE Package: crisprseekplus Version: 1.30.0 Depends: R (>= 3.3.0), shiny, shinyjs, CRISPRseek Imports: DT, utils, GUIDEseq, GenomicRanges, GenomicFeatures, BiocManager, BSgenome, AnnotationDbi, hash Suggests: testthat, rmarkdown, knitr, R.rsp License: GPL-3 + file LICENSE Package: crisprShiny Version: 1.0.0 Depends: R (>= 4.4.0), shiny Imports: BiocGenerics, Biostrings, BSgenome, crisprBase, crisprDesign, crisprScore, crisprViz, DT, GenomeInfoDb, htmlwidgets, methods, pwalign, S4Vectors, shinyBS, shinyjs, utils, waiter Suggests: BiocStyle, knitr, rmarkdown, shinyFeedback, testthat (>= 3.0.0), BSgenome.Hsapiens.UCSC.hg38 License: MIT + file LICENSE Package: CrispRVariants Version: 1.32.0 Depends: R (>= 4.3.0), ggplot2 (>= 2.2.0) Imports: AnnotationDbi, BiocParallel, Biostrings, methods, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>= 0.9.38), utils Suggests: BiocStyle, GenomicFeatures, knitr, rmarkdown, readxl, rtracklayer, sangerseqR, testthat, VariantAnnotation License: GPL-2 Package: crisprVerse Version: 1.6.0 Depends: R (>= 4.2.0) Imports: BiocManager, cli, crisprBase, crisprBowtie, crisprScore, crisprScoreData, crisprDesign, crisprViz, rlang, tools, utils Suggests: BiocStyle, knitr, testthat License: MIT + file LICENSE Package: crisprViz Version: 1.6.0 Depends: R (>= 4.2.0), crisprBase (>= 0.99.15), crisprDesign (>= 0.99.77) Imports: BiocGenerics, Biostrings, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, grDevices, Gviz, IRanges, methods, S4Vectors, txdbmaker Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, rtracklayer, testthat, utils License: MIT + file LICENSE Package: crlmm Version: 1.62.0 Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>= 1.17.7) Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>= 1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1), matrixStats, VGAM, parallel, graphics, limma, beanplot LinkingTo: preprocessCore (>= 1.17.7) Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats, RUnit License: Artistic-2.0 Archs: x64 Package: crossmeta Version: 1.30.0 Depends: R (>= 4.0) Imports: affy (>= 1.52.0), affxparser (>= 1.46.0), AnnotationDbi (>= 1.36.2), Biobase (>= 2.34.0), BiocGenerics (>= 0.20.0), BiocManager (>= 1.30.4), DT (>= 0.2), DBI (>= 1.0.0), data.table (>= 1.10.4), edgeR, fdrtool (>= 1.2.15), GEOquery (>= 2.40.0), limma (>= 3.30.13), matrixStats (>= 0.51.0), metaMA (>= 3.1.2), miniUI (>= 0.1.1), methods, oligo (>= 1.38.0), reader(>= 1.0.6), RCurl (>= 1.95.4.11), RSQLite (>= 2.1.1), stringr (>= 1.2.0), sva (>= 3.22.0), shiny (>= 1.0.0), shinyjs (>= 2.0.0), shinyBS (>= 0.61), shinyWidgets (>= 0.5.3), shinypanel (>= 0.1.0), tibble, XML (>= 3.98.1.17), readxl (>= 1.3.1) Suggests: knitr, rmarkdown, lydata, org.Hs.eg.db, testthat License: MIT + file LICENSE Package: CSAR Version: 1.56.0 Depends: R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges Imports: stats, utils Suggests: ShortRead, Biostrings License: Artistic-2.0 Archs: x64 Package: csaw Version: 1.38.0 Depends: R (>= 3.5.0), GenomicRanges, SummarizedExperiment Imports: Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, methods, S4Vectors, IRanges, GenomeInfoDb, stats, BiocParallel, metapod, utils LinkingTo: Rhtslib, zlibbioc, Rcpp Suggests: AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager License: GPL-3 Archs: x64 Package: csdR Version: 1.10.0 Depends: R (>= 4.1.0) Imports: WGCNA, glue, RhpcBLASctl, matrixStats, Rcpp LinkingTo: Rcpp Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr, igraph, dplyr License: GPL-3 Archs: x64 Package: CSSQ Version: 1.16.0 Depends: SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, rtracklayer Imports: GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2, grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown, markdown License: Artistic-2.0 Package: ctc Version: 1.78.0 Depends: amap License: GPL-2 Package: CTdata Version: 1.4.0 Depends: R (>= 4.2) Imports: ExperimentHub, utils Suggests: testthat (>= 3.0.0), DT, BiocStyle, knitr, rmarkdown, SummarizedExperiment, SingleCellExperiment License: Artistic-2.0 Package: CTDquerier Version: 2.12.0 Depends: R (>= 4.1) Imports: RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils, grid, gridExtra, methods, stats, BiocFileCache Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE Package: CTexploreR Version: 1.0.0 Depends: R (>= 4.3), CTdata Imports: BiocGenerics, ComplexHeatmap, grid, SummarizedExperiment, GenomicRanges, IRanges, dplyr, tidyr, tibble, ggplot2, rlang, grDevices, stats, circlize, ggrepel, SingleCellExperiment, MatrixGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 Package: cTRAP Version: 1.22.0 Depends: R (>= 4.0) Imports: AnnotationDbi, AnnotationHub, binr, cowplot, data.table, dplyr, DT, fastmatch, fgsea, ggplot2, ggrepel, graphics, highcharter, htmltools, httr, limma, methods, parallel, pbapply, purrr, qs, R.utils, readxl, reshape2, rhdf5, rlang, scales, shiny (>= 1.7.0), shinycssloaders, stats, tibble, tools, utils Suggests: testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes License: MIT + file LICENSE Package: ctsGE Version: 1.30.0 Depends: R (>= 3.2) Imports: ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils Suggests: BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown, testthat License: GPL-2 Package: CTSV Version: 1.6.0 Depends: R (>= 4.2), Imports: stats, pscl, qvalue, BiocParallel, methods, knitr, SpatialExperiment, SummarizedExperiment Suggests: testthat, BiocStyle License: GPL-3 Package: cummeRbund Version: 2.46.0 Depends: R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2, reshape2, fastcluster, rtracklayer, Gviz Imports: methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase Suggests: cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson License: Artistic-2.0 Package: CuratedAtlasQueryR Version: 1.2.0 Depends: R (>= 4.2.0) Imports: dplyr, SummarizedExperiment, SingleCellExperiment, purrr (>= 1.0.0), BiocGenerics, glue, HDF5Array, DBI, tools, httr, cli, assertthat, SeuratObject, Seurat, methods, rlang, stats, S4Vectors, tibble, utils, dbplyr (>= 2.3.0), duckdb, stringr Suggests: zellkonverter, rmarkdown, knitr, testthat, basilisk, arrow, reticulate, spelling, forcats, ggplot2, tidySingleCellExperiment, rprojroot License: GPL-3 Package: customCMPdb Version: 1.14.0 Depends: R (>= 4.0) Imports: AnnotationHub, RSQLite, XML, utils, ChemmineR, methods, stats, rappdirs, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 Package: customProDB Version: 1.44.0 Depends: R (>= 3.5.0), IRanges, AnnotationDbi, biomaRt (>= 2.17.1) Imports: S4Vectors (>= 0.9.25), DBI, GenomeInfoDb, GenomicRanges, Rsamtools (>= 1.10.2), GenomicAlignments, Biostrings (>= 2.26.3), GenomicFeatures (>= 1.32.0), stringr, RCurl, plyr, VariantAnnotation (>= 1.13.44), rtracklayer, RSQLite, txdbmaker, AhoCorasickTrie, methods Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 Package: cyanoFilter Version: 1.12.0 Depends: R(>= 4.1.0) Imports: Biobase, flowCore, flowDensity, flowClust, cytometree, ggplot2, GGally, graphics, grDevices, methods, mrfDepth, stats, utils Suggests: magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr License: MIT + file LICENSE Package: cycle Version: 1.58.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats License: GPL-2 Package: cydar Version: 1.28.0 Depends: SingleCellExperiment Imports: viridis, methods, shiny, graphics, stats, grDevices, utils, BiocGenerics, S4Vectors, BiocParallel, SummarizedExperiment, flowCore, Biobase, Rcpp, BiocNeighbors LinkingTo: Rcpp Suggests: ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet, BiocStyle, flowStats License: GPL-3 Archs: x64 Package: cypress Version: 1.0.0 Depends: R(>= 4.4.0) Imports: stats, abind, sirt, MASS,TOAST, tibble, parallel, preprocessCore, SummarizedExperiment, TCA, PROPER, methods,dplyr, utils, RColorBrewer, graphics, edgeR, BiocParallel, checkmate, mvtnorm, DESeq2, rlang, e1071 Suggests: knitr, rmarkdown, MatrixGenerics, htmltools, RUnit, BiocGenerics, BiocManager, BiocStyle, Biobase License: GPL-2 | GPL-3 Package: CytoDx Version: 1.24.0 Depends: R (>= 3.5) Imports: doParallel, dplyr, glmnet, rpart, rpart.plot, stats, flowCore,grDevices, graphics, utils Suggests: knitr, rmarkdown License: GPL-2 Package: cytofQC Version: 1.4.0 Imports: CATALYST, flowCore, e1071, EZtune, gbm, ggplot2, hrbrthemes, matrixStats, randomForest, rmarkdown, SingleCellExperiment, stats, SummarizedExperiment, ssc, S4Vectors, graphics, methods Suggests: gridExtra, knitr, RColorBrewer, testthat, uwot License: Artistic-2.0 Package: CytoGLMM Version: 1.12.0 Imports: stats, methods, BiocParallel, RColorBrewer, cowplot, doParallel, dplyr, factoextra, flexmix, ggplot2, magrittr, mbest, pheatmap, stringr, strucchange, tibble, ggrepel, MASS, logging, Matrix, tidyr, caret, rlang, grDevices Suggests: knitr, rmarkdown, testthat, BiocStyle License: LGPL-3 Package: cytoKernel Version: 1.10.0 Depends: R (>= 4.1) Imports: Rcpp, SummarizedExperiment, utils, methods, ComplexHeatmap, circlize, ashr, data.table, BiocParallel, dplyr, stats, magrittr, rlang, S4Vectors LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 Archs: x64 Package: cytolib Version: 2.16.0 Depends: R (>= 3.4) Imports: RProtoBufLib LinkingTo: BH(>= 1.84.0.0), RProtoBufLib(>= 2.13.1),Rhdf5lib Suggests: knitr, rmarkdown License_restricts_use: no Archs: x64 Package: cytomapper Version: 1.16.0 Depends: R (>= 4.0), EBImage, SingleCellExperiment, methods Imports: SpatialExperiment, S4Vectors, BiocParallel, HDF5Array, DelayedArray, RColorBrewer, viridis, utils, SummarizedExperiment, tools, graphics, raster, grDevices, stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny, shinydashboard, matrixStats, rhdf5, nnls Suggests: BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat, shinytest License: GPL (>= 2) Package: CytoMDS Version: 1.0.0 Depends: R (>= 4.3) Imports: methods, stats, rlang, pracma, withr, flowCore, reshape2, ggplot2, ggrepel, ggforce, patchwork, transport, smacof, BiocParallel, CytoPipeline Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, HDCytoData License: GPL-3 Package: cytoMEM Version: 1.8.0 Depends: R (>= 4.2.0) Imports: gplots, tools, flowCore, grDevices, stats, utils, matrixStats, methods Suggests: knitr, rmarkdown License: GPL-3 Package: CytoML Version: 2.16.0 Depends: R (>= 3.5.0) Imports: cytolib(>= 2.3.10), flowCore (>= 1.99.10), flowWorkspace (>= 4.1.8), openCyto (>= 1.99.2), XML, data.table, jsonlite, RBGL, Rgraphviz, Biobase, methods, graph, graphics, utils, jsonlite, dplyr, grDevices, methods, ggcyto (>= 1.11.4), yaml, stats, tibble LinkingTo: cpp11, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib, flowWorkspace Suggests: testthat, flowWorkspaceData , knitr, rmarkdown, parallel License_restricts_use: no Archs: x64 Package: CytoPipeline Version: 1.4.0 Depends: R (>= 4.3) Imports: methods, stats, utils, withr, rlang, ggplot2 (>= 3.4.1), ggcyto, BiocFileCache, BiocParallel, flowCore, PeacoQC, flowAI, diagram, jsonlite, scales Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, reshape2, dplyr License: GPL-3 Package: CytoPipelineGUI Version: 1.2.0 Depends: R (>= 4.3), CytoPipeline Imports: shiny, plotly, ggplot2, flowCore Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, patchwork License: GPL-3 Package: cytoviewer Version: 1.4.0 Imports: shiny, shinydashboard, utils, colourpicker, shinycssloaders, svgPanZoom, viridis, archive, grDevices, RColorBrewer, svglite, EBImage, methods, cytomapper, SingleCellExperiment, S4Vectors, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat License: GPL-3 Package: dada2 Version: 1.32.0 Depends: R (>= 3.4.0), Rcpp (>= 0.12.0), methods (>= 3.4.0) Imports: Biostrings (>= 2.42.1), ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), ShortRead (>= 1.32.0), RcppParallel (>= 4.3.0), parallel (>= 3.2.0), IRanges (>= 2.6.0), XVector (>= 0.16.0), BiocGenerics (>= 0.22.0) LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, knitr, rmarkdown License: LGPL-2 Archs: x64 Package: dagLogo Version: 1.42.0 Depends: R (>= 3.0.1), methods, grid Imports: pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils, biomaRt, motifStack, httr Suggests: XML, grImport, grImport2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) Package: daMA Version: 1.76.0 Imports: MASS, stats License: GPL (>= 2) Package: DAMEfinder Version: 1.16.0 Depends: R (>= 4.0) Imports: stats, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, readr, SummarizedExperiment, GenomicAlignments, stringr, plyr, VariantAnnotation, parallel, ggplot2, Rsamtools, BiocGenerics, methods, limma, bumphunter, Biostrings, reshape2, cowplot, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE Package: DaMiRseq Version: 2.16.0 Depends: R (>= 3.5.0), SummarizedExperiment, ggplot2 Imports: DESeq2, limma, EDASeq, RColorBrewer, sva, Hmisc, pheatmap, FactoMineR, corrplot, randomForest, e1071, caret, MASS, lubridate, plsVarSel, kknn, FSelector, methods, stats, utils, graphics, grDevices, reshape2, ineq, arm, pls, RSNNS, edgeR, plyr Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) Package: Damsel Version: 1.0.0 Depends: R (>= 4.4.0) Imports: AnnotationDbi, Biostrings, dplyr, edgeR, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggbio, ggplot2, goseq, magrittr, patchwork, plyranges, reshape2, rlang, Rsamtools, Rsubread, stats, stringr, tidyr, utils Suggests: BiocStyle, biomaRt, biovizBase, BSgenome.Dmelanogaster.UCSC.dm6, knitr, limma, org.Dm.eg.db, rmarkdown, testthat (>= 3.0.0), TxDb.Dmelanogaster.UCSC.dm6.ensGene License: MIT + file LICENSE Package: DAPAR Version: 1.36.2 Depends: R (>= 4.3.0) Imports: Biobase, MSnbase, DAPARdata (>= 1.30.0), utils, highcharter, foreach Suggests: testthat, BiocStyle, AnnotationDbi, clusterProfiler, graph, diptest, cluster, vioplot, visNetwork, vsn, igraph, FactoMineR, factoextra, dendextend, parallel, doParallel, Mfuzz, apcluster, forcats, readxl, openxlsx, multcomp, purrr, tibble, knitr, norm, scales, tidyverse, cp4p, imp4p (>= 1.1),lme4, dplyr, limma, preprocessCore, stringr, tidyr, impute, gplots, grDevices, reshape2, graphics, stats, methods, ggplot2, RColorBrewer, Matrix, org.Sc.sgd.db License: Artistic-2.0 Package: dar Version: 1.0.0 Depends: R (>= 4.4.0) Imports: cli, ComplexHeatmap, crayon, dplyr, generics, ggplot2, glue, gplots, heatmaply, magrittr, methods, mia, phyloseq, purrr, readr, rlang (>= 0.4.11), scales, stringr, tibble, tidyr, UpSetR, waldo Suggests: ALDEx2, ANCOMBC, apeglm, ashr, Biobase, corncob, covr, DESeq2, devtools, furrr, future, knitr, lefser, limma, Maaslin2, metagenomeSeq, microbiome, rmarkdown, roxygen2, roxyglobals, roxytest, rstatix, SummarizedExperiment, TreeSummarizedExperiment, testthat (>= 3.0.0) License: MIT + file LICENSE Package: DART Version: 1.52.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 Package: dcanr Version: 1.20.0 Depends: R (>= 3.6.0) Imports: igraph, foreach, plyr, stringr, reshape2, methods, Matrix, graphics, stats, RColorBrewer, circlize, doRNG Suggests: EBcoexpress, testthat, EBarrays, GeneNet, mclust, minqa, SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle, edgeR Enhances: parallel, doSNOW, doParallel License: GPL-3 Package: DCATS Version: 1.2.0 Depends: R (>= 4.1.0), stats Imports: MCMCpack, matrixStats, robustbase, aod, e1071 Suggests: testthat (>= 3.0.0), knitr, Seurat, SeuratObject, tidyverse, rmarkdown, BiocStyle License: MIT + file LICENSE Package: dce Version: 1.12.0 Depends: R (>= 4.1) Imports: stats, methods, assertthat, graph, pcalg, purrr, tidyverse, Matrix, ggraph, tidygraph, ggplot2, rlang, expm, MASS, edgeR, epiNEM, igraph, metap, mnem, naturalsort, ppcor, glm2, graphite, reshape2, dplyr, magrittr, glue, Rgraphviz, harmonicmeanp, org.Hs.eg.db, logger, shadowtext Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, cowplot, ggplotify, dagitty, lmtest, sandwich, devtools, curatedTCGAData, TCGAutils, SummarizedExperiment, RcppParallel, docopt, CARNIVAL License: GPL-3 Package: dcGSA Version: 1.32.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 Package: ddCt Version: 1.60.0 Depends: R (>= 2.3.0), methods Imports: Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, BiocGenerics Suggests: testthat (>= 3.0.0), RUnit License: LGPL-3 Package: ddPCRclust Version: 1.24.0 Depends: R (>= 3.5) Imports: plotrix, clue, parallel, ggplot2, openxlsx, R.utils, flowCore, flowDensity (>= 1.13.3), SamSPECTRAL, flowPeaks Suggests: BiocStyle License: Artistic-2.0 Package: dearseq Version: 1.16.0 Depends: R (>= 3.6.0) Imports: CompQuadForm, dplyr, ggplot2, KernSmooth, magrittr, matrixStats, methods, patchwork, parallel, pbapply, reshape2, rlang, scattermore, stats, statmod, survey, tibble, viridisLite Suggests: Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA, knitr, limma, readxl, rmarkdown, S4Vectors, SummarizedExperiment, testthat, covr License: GPL-2 | file LICENSE Package: debCAM Version: 1.22.0 Depends: R (>= 3.5) Imports: methods, rJava, BiocParallel, stats, Biobase, SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR2, pcaPP, apcluster, graphics Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl License: GPL-2 Package: debrowser Version: 1.32.0 Depends: R (>= 3.5.0), Imports: shiny, jsonlite, shinyjs, shinydashboard, shinyBS, gplots, DT, ggplot2, RColorBrewer, annotate, AnnotationDbi, DESeq2, DOSE, igraph, grDevices, graphics, stats, utils, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2, org.Hs.eg.db, org.Mm.eg.db, limma, edgeR, clusterProfiler, methods, sva, RCurl, enrichplot, colourpicker, plotly, heatmaply, Harman, pathview, apeglm, ashr Suggests: testthat, rmarkdown, knitr License: GPL-3 + file LICENSE Package: DECIPHER Version: 3.0.0 Depends: R (>= 3.5.0), Biostrings (>= 2.59.1), stats Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, S4Vectors, IRanges, XVector Suggests: RSQLite (>= 1.1) License: GPL-3 Archs: x64 Package: decompTumor2Sig Version: 2.20.0 Depends: R(>= 4.0), ggplot2 Imports: methods, Matrix, quadprog(>= 1.5-5), GenomicRanges, stats, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, SummarizedExperiment, ggseqlogo, gridExtra, data.table, GenomeInfoDb, readxl Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 Package: DeconRNASeq Version: 1.46.0 Depends: R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid License: GPL-2 Package: decontam Version: 1.24.0 Depends: R (>= 3.4.1), methods (>= 3.4.1) Imports: ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), stats Suggests: BiocStyle, knitr, rmarkdown, phyloseq License: Artistic-2.0 Package: decontX Version: 1.2.0 Depends: R (>= 4.3.0) Imports: celda, dbscan, DelayedArray, ggplot2, Matrix (>= 1.5.3), MCMCprecision, methods, patchwork, plyr, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.2.0), S4Vectors, scater, Seurat, SingleCellExperiment, SummarizedExperiment, withr LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, dplyr, knitr, rmarkdown, scran, SingleCellMultiModal, TENxPBMCData, testthat (>= 3.0.0) License: MIT + file LICENSE Archs: x64 Package: deconvR Version: 1.10.0 Depends: R (>= 4.1), data.table (>= 1.14.0) Imports: S4Vectors (>= 0.30.0), methylKit (>= 1.18.0), IRanges (>= 2.26.0), GenomicRanges (>= 1.44.0), BiocGenerics (>= 0.38.0), stats, methods, foreach (>= 1.5.1), magrittr (>= 2.0.1), matrixStats (>= 0.61.0), e1071 (>= 1.7.9), quadprog (>= 1.5.8), nnls (>= 1.4), rsq (>= 2.2), MASS, utils, dplyr (>= 1.0.7), tidyr (>= 1.1.3), assertthat, minfi Suggests: testthat (>= 3.0.0), roxygen2 (>= 7.1.2), doParallel (>= 1.0.16), parallel, knitr (>= 1.34), BiocStyle (>= 2.20.2), reshape2 (>= 1.4.4), ggplot2 (>= 3.3.5), rmarkdown, devtools (>= 2.4.2), sessioninfo (>= 1.1.1), covr, granulator, RefManageR License: Artistic-2.0 Package: decoupleR Version: 2.10.0 Depends: R (>= 4.0) Imports: BiocParallel, broom, dplyr, magrittr, Matrix, parallelly, purrr, rlang, stats, stringr, tibble, tidyr, tidyselect, withr Suggests: glmnet (>= 4.1-7), GSVA, viper, fgsea (>= 1.15.4), AUCell, SummarizedExperiment, rpart, ranger, BiocStyle, covr, knitr, pkgdown, RefManageR, rmarkdown, roxygen2, sessioninfo, pheatmap, testthat, OmnipathR, Seurat, ggplot2, ggrepel, patchwork, magick License: GPL-3 + file LICENSE Package: DeepPINCS Version: 1.12.0 Depends: keras, R (>= 4.1) Imports: tensorflow, CatEncoders, matlab, rcdk, stringdist, tokenizers, webchem, purrr, ttgsea, PRROC, reticulate, stats Suggests: knitr, testthat, rmarkdown License: Artistic-2.0 Package: deepSNV Version: 1.50.0 Depends: R (>= 2.13.0), methods, graphics, parallel, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation (>= 1.27.6), Imports: Rhtslib LinkingTo: Rhtslib (>= 1.13.1) Suggests: RColorBrewer, knitr, rmarkdown License: GPL-3 Archs: x64 Package: DEFormats Version: 1.32.0 Imports: checkmate, data.table, DESeq2, edgeR (>= 3.13.4), GenomicRanges, methods, S4Vectors, stats, SummarizedExperiment Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat License: GPL-3 Package: DegCre Version: 1.0.0 Depends: R (>= 4.4) Imports: GenomicRanges, InteractionSet, plotgardener, S4Vectors, stats, graphics, grDevices, BiocGenerics, GenomeInfoDb, IRanges, utils Suggests: BSgenome, BSgenome.Hsapiens.UCSC.hg38, org.Hs.eg.db, BiocStyle, magick, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat (>= 3.0.0) License: MIT + file LICENSE Package: DegNorm Version: 1.14.0 Depends: R (>= 4.0.0), methods Imports: Rcpp (>= 1.0.2),GenomicFeatures, txdbmaker, parallel, foreach, S4Vectors, doParallel, Rsamtools (>= 1.31.2), GenomicAlignments, heatmaply, data.table, stats, ggplot2, GenomicRanges, IRanges, plyr, plotly, utils,viridis LinkingTo: Rcpp, RcppArmadillo,S4Vectors,IRanges Suggests: knitr,rmarkdown,formatR License: LGPL (>= 3) Archs: x64 Package: DEGreport Version: 1.40.1 Depends: R (>= 4.0.0) Imports: utils, methods, Biobase, BiocGenerics, broom, circlize, ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster, dendextend, DESeq2, dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices, knitr, logging, magrittr, psych, RColorBrewer, reshape, rlang, scales, stats, stringr, stringi, S4Vectors, SummarizedExperiment, tidyr, tibble Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat License: MIT + file LICENSE Package: DEGseq Version: 1.58.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) Archs: x64 Package: DelayedArray Version: 0.30.1 Depends: R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>= 0.43.4), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.27.2), IRanges (>= 2.17.3), S4Arrays (>= 1.3.5), SparseArray (>= 1.1.10) Imports: stats LinkingTo: S4Vectors Suggests: BiocParallel, HDF5Array (>= 1.17.12), genefilter, SummarizedExperiment, airway, lobstr, DelayedMatrixStats, knitr, rmarkdown, BiocStyle, RUnit License: Artistic-2.0 Archs: x64 Package: DelayedDataFrame Version: 1.20.0 Depends: R (>= 3.6), S4Vectors (>= 0.23.19), DelayedArray (>= 0.7.5) Imports: methods, stats, BiocGenerics Suggests: testthat, knitr, rmarkdown, BiocStyle, SeqArray, GDSArray License: GPL-3 Package: DelayedMatrixStats Version: 1.26.0 Depends: MatrixGenerics (>= 1.15.1), DelayedArray (>= 0.27.10) Imports: methods, sparseMatrixStats (>= 1.13.2), Matrix (>= 1.5-0), S4Vectors (>= 0.17.5), IRanges (>= 2.25.10) Suggests: testthat, knitr, rmarkdown, BiocStyle, microbenchmark, profmem, HDF5Array, matrixStats (>= 1.0.0) License: MIT + file LICENSE Package: DelayedRandomArray Version: 1.12.0 Depends: DelayedArray (>= 0.27.2) Imports: methods, dqrng, Rcpp LinkingTo: dqrng, BH, Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, Matrix License: GPL-3 Archs: x64 Package: DelayedTensor Version: 1.10.0 Depends: R (>= 4.1.0) Imports: methods, utils, DelayedArray, HDF5Array, BiocSingular, rTensor, DelayedRandomArray, irlba, Matrix, einsum, Suggests: markdown, rmarkdown, BiocStyle, knitr, testthat, magrittr, dplyr, reticulate License: Artistic-2.0 Package: DELocal Version: 1.4.0 Imports: DESeq2, dplyr, reshape2, limma, SummarizedExperiment, ggplot2, matrixStats, stats Suggests: biomaRt, knitr, rmarkdown, stringr, BiocStyle License: MIT + file LICENSE Package: deltaCaptureC Version: 1.18.0 Depends: R (>= 3.6) Imports: IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2, tictoc Suggests: knitr, rmarkdown License: MIT + file LICENSE Package: deltaGseg Version: 1.44.0 Depends: R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh, tseries, pvclust, fBasics, grid, reshape, scales Suggests: knitr License: GPL-2 Package: DeMAND Version: 1.34.0 Depends: R (>= 2.14.0), KernSmooth, methods License: file LICENSE Package: DeMixT Version: 1.20.0 Depends: R (>= 3.6.0), parallel, Rcpp (>= 1.0.0), SummarizedExperiment, knitr, KernSmooth, matrixcalc, rmarkdown, DSS, dendextend, psych, sva Imports: matrixStats, stats, truncdist, base64enc, ggplot2 LinkingTo: Rcpp License: GPL-3 Archs: x64 Package: demuxmix Version: 1.6.0 Depends: R (>= 4.0.0) Imports: stats, MASS, Matrix, ggplot2, gridExtra, methods Suggests: BiocStyle, cowplot, DropletUtils, knitr, reshape2, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 Package: demuxSNP Version: 1.2.0 Depends: R (>= 4.3.0), SingleCellExperiment, VariantAnnotation, ensembldb Imports: MatrixGenerics, BiocGenerics, class, GenomeInfoDb, IRanges, Matrix, SummarizedExperiment, demuxmix, methods, KernelKnn, dplyr Suggests: knitr, rmarkdown, ComplexHeatmap, viridisLite, ggpubr, dittoSeq, EnsDb.Hsapiens.v86, BiocStyle, RefManageR, testthat (>= 3.0.0), Seurat License: GPL-3 Package: densvis Version: 1.14.0 Imports: Rcpp, basilisk, assertthat, reticulate, Rtsne, irlba LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, ggplot2, uwot, testthat License: MIT + file LICENSE Archs: x64 Package: DEP Version: 1.26.0 Depends: R (>= 3.5) Imports: ggplot2, dplyr, purrr, readr, tibble, tidyr, SummarizedExperiment (>= 1.11.5), MSnbase, limma, vsn, fdrtool, ggrepel, ComplexHeatmap, RColorBrewer, circlize, shiny, shinydashboard, DT, rmarkdown, assertthat, gridExtra, grid, stats, imputeLCMD, cluster Suggests: testthat, enrichR, knitr, BiocStyle License: Artistic-2.0 Package: DepecheR Version: 1.20.0 Depends: R (>= 4.0) Imports: ggplot2 (>= 3.1.0), MASS (>= 7.3.51), Rcpp (>= 1.0.0), dplyr (>= 0.7.8), gplots (>= 3.0.1), viridis (>= 0.5.1), foreach (>= 1.4.4), doSNOW (>= 1.0.16), matrixStats (>= 0.54.0), mixOmics (>= 6.6.1), moments (>= 0.14), grDevices (>= 3.5.2), graphics (>= 3.5.2), stats (>= 3.5.2), utils (>= 3.5), methods (>= 3.5), parallel (>= 3.5.2), reshape2 (>= 1.4.3), beanplot (>= 1.2), FNN (>= 1.1.3), robustbase (>= 0.93.5), gmodels (>= 2.18.1), collapse (>= 1.9.2), ClusterR (>= 1.3.2) LinkingTo: Rcpp, RcppEigen Suggests: uwot, testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE Archs: x64 Package: DepInfeR Version: 1.8.0 Depends: R (>= 4.2.0) Imports: matrixStats, glmnet, stats, BiocParallel Suggests: testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, tibble, ggplot2, missForest, pheatmap, RColorBrewer, ggrepel, BiocStyle, ggbeeswarm License: GPL-3 Package: DeProViR Version: 1.0.0 Depends: keras Imports: caret, data.table, dplyr, fmsb, ggplot2, grDevices, pROC, PRROC, readr, stats, BiocFileCache, utils Suggests: rmarkdown, tensorflow, BiocStyle, RUnit, knitr, BiocGenerics License: MIT + file LICENSE Package: DEqMS Version: 1.22.0 Depends: R(>= 3.5),graphics,stats,ggplot2,matrixStats,limma(>= 3.34) Suggests: BiocStyle,knitr,rmarkdown,markdown,plyr,reshape2,farms,utils,ggrepel,ExperimentHub,LSD License: LGPL Package: derfinder Version: 1.38.0 Depends: R (>= 3.5.0) Imports: BiocGenerics (>= 0.25.1), AnnotationDbi (>= 1.27.9), BiocParallel (>= 1.15.15), bumphunter (>= 1.9.2), derfinderHelper (>= 1.1.0), GenomeInfoDb (>= 1.3.3), GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges (>= 1.17.40), Hmisc, IRanges (>= 2.3.23), methods, qvalue (>= 1.99.0), Rsamtools (>= 1.25.0), rtracklayer, S4Vectors (>= 0.23.19), stats, utils Suggests: BiocStyle (>= 2.5.19), sessioninfo, derfinderData (>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitr (>= 1.6), limma, RefManageR, rmarkdown (>= 0.3.3), testthat (>= 2.1.0), TxDb.Hsapiens.UCSC.hg19.knownGene, covr License: Artistic-2.0 Package: derfinderHelper Version: 1.38.0 Depends: R(>= 3.2.2) Imports: IRanges (>= 1.99.27), Matrix, methods, S4Vectors (>= 0.2.2) Suggests: sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19), RefManageR, rmarkdown (>= 0.3.3), testthat, covr License: Artistic-2.0 Package: derfinderPlot Version: 1.38.0 Depends: R(>= 3.2) Imports: derfinder (>= 1.1.0), GenomeInfoDb (>= 1.3.3), GenomicFeatures, GenomicRanges (>= 1.17.40), ggbio (>= 1.13.13), ggplot2, graphics, grDevices, IRanges (>= 1.99.28), limma, methods, plyr, RColorBrewer, reshape2, S4Vectors (>= 0.9.38), scales, utils Suggests: biovizBase (>= 1.27.2), bumphunter (>= 1.7.6), derfinderData (>= 0.99.0), sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19), org.Hs.eg.db, RefManageR, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, covr License: Artistic-2.0 Package: DEScan2 Version: 1.24.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocParallel, BiocGenerics, ChIPpeakAnno, data.table, DelayedArray, GenomeInfoDb, GenomicAlignments, glue, IRanges, plyr, Rcpp (>= 0.12.13), rtracklayer, S4Vectors (>= 0.23.19), SummarizedExperiment, tools, utils LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod License: Artistic-2.0 Archs: x64 Package: DESeq2 Version: 1.44.0 Depends: S4Vectors (>= 0.23.18), IRanges, GenomicRanges, SummarizedExperiment (>= 1.1.6) Imports: BiocGenerics (>= 0.7.5), Biobase, BiocParallel, matrixStats, methods, stats4, locfit, ggplot2 (>= 3.4.0), Rcpp (>= 0.11.0), MatrixGenerics LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, pasilla (>= 0.2.10), glmGamPoi, BiocManager License: LGPL (>= 3) Archs: x64 Package: DEsingle Version: 1.24.0 Depends: R (>= 3.4.0) Imports: stats, Matrix (>= 1.2-14), MASS (>= 7.3-45), VGAM (>= 1.0-2), bbmle (>= 1.0.18), gamlss (>= 4.4-0), maxLik (>= 1.3-4), pscl (>= 1.4.9), BiocParallel (>= 1.12.0), Suggests: knitr, rmarkdown, SingleCellExperiment License: GPL-2 Package: DESpace Version: 1.4.0 Depends: R (>= 4.3.0) Imports: edgeR, limma, dplyr, stats, Matrix, SpatialExperiment, ggplot2, ggpubr, scales, SummarizedExperiment, S4Vectors, BiocGenerics, data.table, assertthat, cowplot, ggforce, ggnewscale, patchwork, BiocParallel, methods Suggests: knitr, rmarkdown, testthat, BiocStyle, ExperimentHub, concaveman, spatialLIBD, purrr, scuttle, utils License: GPL-3 Package: destiny Version: 3.18.0 Depends: R (>= 3.4.0) Imports: methods, graphics, grDevices, grid, utils, stats, Matrix, Rcpp (>= 0.10.3), RcppEigen, RSpectra (>= 0.14-0), irlba, pcaMethods, Biobase, BiocGenerics, SummarizedExperiment, SingleCellExperiment, ggplot2, ggplot.multistats, rlang, tidyr, tidyselect, ggthemes, VIM, knn.covertree, proxy, RcppHNSW, smoother, scales, scatterplot3d LinkingTo: Rcpp, RcppEigen, grDevices Suggests: knitr, rmarkdown, igraph, testthat, FNN, tidyverse, gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq, org.Mm.eg.db, scran, repr Enhances: rgl, SingleCellExperiment License: GPL-3 Archs: x64 Package: DEsubs Version: 1.30.0 Depends: R (>= 3.3), locfit Imports: graph, igraph, RBGL, circlize, limma, edgeR, EBSeq, NBPSeq, stats, grDevices, graphics, pheatmap, utils, ggplot2, Matrix, jsonlite, tools, DESeq2, methods Suggests: RUnit, BiocGenerics, knitr, rmarkdown License: GPL-3 Package: DEWSeq Version: 1.18.0 Depends: R(>= 4.0.0), R.utils, DESeq2, BiocParallel Imports: BiocGenerics, data.table(>= 1.11.8), GenomeInfoDb, GenomicRanges, methods, S4Vectors, SummarizedExperiment, stats, utils Suggests: knitr, tidyverse, rmarkdown, testthat, BiocStyle, IHW License: LGPL (>= 3) Package: DExMA Version: 1.12.0 Depends: R (>= 4.1), DExMAdata Imports: Biobase, GEOquery, impute, limma, pheatmap, plyr, scales, snpStats, sva, swamp, stats, methods, utils, bnstruct, RColorBrewer, grDevices Suggests: BiocStyle, qpdf, BiocGenerics, RUnit License: GPL-2 Package: DEXSeq Version: 1.50.0 Depends: BiocParallel, Biobase, SummarizedExperiment, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), DESeq2 (>= 1.39.6), AnnotationDbi, RColorBrewer, S4Vectors (>= 0.23.18) Imports: BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools, statmod, geneplotter, genefilter Suggests: GenomicFeatures, txdbmaker, pasilla (>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown, testthat, pasillaBamSubset, GenomicAlignments, roxygen2, glmGamPoi License: GPL (>= 3) Package: DFP Version: 1.62.0 Depends: methods, Biobase (>= 2.5.5) License: GPL-2 Package: DIAlignR Version: 2.12.0 Depends: methods, stats, R (>= 4.0) Imports: zoo (>= 1.8-3), data.table, magrittr, dplyr, tidyr, rlang, mzR (>= 2.18), signal, bit64, reticulate, ggplot2, RSQLite, DBI, ape, phangorn, pracma, RMSNumpress, Rcpp LinkingTo: Rcpp, RcppEigen Suggests: knitr, akima, lattice, scales, gridExtra, latticeExtra, rmarkdown, BiocStyle, BiocParallel, testthat (>= 2.1.0) License: GPL-3 Archs: x64 Package: DiffBind Version: 3.14.0 Depends: R (>= 4.0), GenomicRanges, SummarizedExperiment Imports: RColorBrewer, amap, gplots, grDevices, limma, GenomicAlignments, locfit, stats, utils, IRanges, lattice, systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel, parallel, S4Vectors, Rsamtools (>= 2.13.1), DESeq2, methods, graphics, ggrepel, apeglm, ashr, GreyListChIP LinkingTo: Rhtslib (>= 1.99.1), Rcpp Suggests: BiocStyle, testthat, xtable, rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid License: Artistic-2.0 Archs: x64 Package: diffcoexp Version: 1.24.0 Depends: R (>= 3.5), WGCNA, SummarizedExperiment Imports: stats, DiffCorr, psych, igraph, BiocGenerics Suggests: GEOquery, RUnit License: GPL (> 2) Package: diffcyt Version: 1.24.0 Depends: R (>= 3.4.0) Imports: flowCore, FlowSOM, SummarizedExperiment, S4Vectors, limma, edgeR, lme4, multcomp, dplyr, tidyr, reshape2, magrittr, stats, methods, utils, grDevices, graphics, ComplexHeatmap, circlize, grid Suggests: BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST License: MIT + file LICENSE Package: DifferentialRegulation Version: 2.2.0 Depends: R (>= 4.3.0) Imports: methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, stats, BANDITS, Matrix, SingleCellExperiment, SummarizedExperiment, ggplot2, tximport, gridExtra LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 Archs: x64 Package: diffGeneAnalysis Version: 1.86.0 Imports: graphics, grDevices, minpack.lm (>= 1.0-4), stats, utils License: GPL Package: diffHic Version: 1.36.1 Depends: R (>= 3.5), GenomicRanges, InteractionSet, SummarizedExperiment Imports: Rsamtools, Rhtslib, Biostrings, BSgenome, rhdf5, edgeR, limma, csaw, locfit, methods, IRanges, S4Vectors, GenomeInfoDb, BiocGenerics, grDevices, graphics, stats, utils, Rcpp, rtracklayer LinkingTo: Rhtslib (>= 1.13.1), zlibbioc, Rcpp Suggests: BSgenome.Ecoli.NCBI.20080805, Matrix, testthat License: GPL-3 Archs: x64 Package: DiffLogo Version: 2.28.0 Depends: R (>= 3.4), stats, cba Imports: grDevices, graphics, utils, tools Suggests: knitr, testthat, seqLogo, MotifDb License: GPL (>= 2) Package: diffuStats Version: 1.24.0 Depends: R (>= 3.4) Imports: grDevices, stats, methods, Matrix, MASS, checkmate, expm, igraph, Rcpp, RcppArmadillo, RcppParallel, plyr, precrec LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata, BiocStyle, reshape2, utils License: GPL-3 Archs: x64 Package: diffUTR Version: 1.12.0 Depends: R (>= 4.0) Imports: S4Vectors, SummarizedExperiment, limma, edgeR, DEXSeq, GenomicRanges, Rsubread, ggplot2, rtracklayer, ComplexHeatmap, ggrepel, stringi, methods, stats, GenomeInfoDb, dplyr, matrixStats, IRanges, ensembldb, viridisLite Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 Package: diggit Version: 1.36.0 Depends: R (>= 3.0.2), Biobase, methods Imports: ks, viper(>= 1.3.1), parallel Suggests: diggitdata License: file LICENSE Package: Dino Version: 1.10.0 Depends: R (>= 4.0.0) Imports: BiocParallel, BiocSingular, SummarizedExperiment, SingleCellExperiment, S4Vectors, Matrix, Seurat, matrixStats, parallel, scran, grDevices, stats, methods Suggests: testthat (>= 2.1.0), knitr, rmarkdown, BiocStyle, devtools, ggplot2, gridExtra, ggpubr, grid, magick, hexbin License: GPL-3 Package: dinoR Version: 1.0.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, edgeR, GenomicRanges, ggplot2, Matrix, methods, rlang, stats, stringr, tibble, tidyr, tidyselect Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE Package: Director Version: 1.30.0 Depends: R (>= 4.0) Imports: htmltools, utils, grDevices License: GPL-3 + file LICENSE Package: dir.expiry Version: 1.12.0 Imports: utils, filelock Suggests: rmarkdown, knitr, testthat, BiocStyle License: GPL-3 Package: DirichletMultinomial Version: 1.46.0 Depends: S4Vectors, IRanges Imports: stats4, methods, BiocGenerics Suggests: lattice, parallel, MASS, RColorBrewer, xtable License: LGPL-3 Archs: x64 Package: discordant Version: 1.28.0 Depends: R (>= 4.1.0) Imports: Rcpp, Biobase, stats, biwt, gtools, MASS, tools, dplyr, methods, utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat (>= 3.0.0) License: GPL-3 Archs: x64 Package: DiscoRhythm Version: 1.20.0 Depends: R (>= 3.6.0) Imports: matrixTests, matrixStats, MetaCycle (>= 1.2.0), data.table, ggplot2, ggExtra, dplyr, broom, shiny, shinyBS, shinycssloaders, shinydashboard, shinyjs, BiocStyle, rmarkdown, knitr, kableExtra, magick, VennDiagram, UpSetR, heatmaply, viridis, plotly, DT, gridExtra, methods, stats, SummarizedExperiment, BiocGenerics, S4Vectors, zip, reshape2 Suggests: testthat License: GPL-3 Package: distinct Version: 1.16.0 Depends: R (>= 4.3) Imports: Rcpp, stats, SummarizedExperiment, SingleCellExperiment, methods, Matrix, foreach, parallel, doParallel, doRNG, ggplot2, limma, scater LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, UpSetR, BiocStyle License: GPL (>= 3) Archs: x64 Package: dittoSeq Version: 1.16.0 Depends: ggplot2 Imports: methods, colorspace (>= 1.4), gridExtra, cowplot, reshape2, pheatmap, grDevices, ggrepel, ggridges, stats, utils, SummarizedExperiment, SingleCellExperiment, S4Vectors Suggests: plotly, testthat, Seurat (>= 2.2), DESeq2, edgeR, ggplot.multistats, knitr, rmarkdown, BiocStyle, scRNAseq, ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran License: MIT + file LICENSE Package: divergence Version: 1.20.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown License: GPL-2 Package: dks Version: 1.50.0 Depends: R (>= 2.8) Imports: cubature License: GPL Package: DMCFB Version: 1.18.0 Depends: R (>= 4.0.0), SummarizedExperiment, methods, S4Vectors, BiocParallel, GenomicRanges, IRanges Imports: utils, stats, speedglm, MASS, data.table, splines, arm, rtracklayer, benchmarkme, tibble, matrixStats, fastDummies, graphics Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 Package: DMCHMM Version: 1.26.0 Depends: R (>= 4.1.0), SummarizedExperiment, methods, S4Vectors, BiocParallel, GenomicRanges, IRanges, fdrtool Imports: utils, stats, grDevices, rtracklayer, multcomp, calibrate, graphics Suggests: testthat, knitr, rmarkdown License: GPL-3 Package: DMRcaller Version: 1.36.0 Depends: R (>= 3.5), GenomicRanges, IRanges, S4Vectors (>= 0.23.10) Imports: parallel, Rcpp, RcppRoll, betareg, grDevices, graphics, methods, stats, utils Suggests: knitr, RUnit, BiocGenerics License: GPL-3 Package: DMRScan Version: 1.26.0 Depends: R (>= 3.6.0) Imports: Matrix, MASS, RcppRoll,GenomicRanges, IRanges, GenomeInfoDb, methods, mvtnorm, stats, parallel Suggests: knitr, rmarkdown, BiocStyle, BiocManager License: GPL-3 Package: dmrseq Version: 1.24.0 Depends: R (>= 3.5), bsseq Imports: GenomicRanges, nlme, ggplot2, S4Vectors, RColorBrewer, bumphunter, DelayedMatrixStats (>= 1.1.13), matrixStats, BiocParallel, outliers, methods, locfit, IRanges, grDevices, graphics, stats, utils, annotatr, AnnotationHub, rtracklayer, GenomeInfoDb, splines Suggests: knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: MIT + file LICENSE Package: DNABarcodeCompatibility Version: 1.20.0 Depends: R (>= 3.6.0) Imports: dplyr, tidyr, numbers, purrr, stringr, DNABarcodes, stats, utils, methods Suggests: knitr, rmarkdown, BiocStyle, testthat License: file LICENSE Package: DNABarcodes Version: 1.34.0 Depends: Matrix, parallel Imports: Rcpp (>= 0.11.2), BH LinkingTo: Rcpp, BH Suggests: knitr, BiocStyle, rmarkdown License: GPL-2 Archs: x64 Package: DNAcopy Version: 1.78.0 License: GPL (>= 2) Archs: x64 Package: DNAfusion Version: 1.6.0 Depends: R (>= 4.2.0) Imports: bamsignals, GenomicRanges, IRanges, Rsamtools, GenomicAlignments, BiocBaseUtils, S4Vectors, GenomicFeatures, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocGenerics Suggests: knitr, rmarkdown, testthat, sessioninfo, BiocStyle License: GPL-3 Package: DNAshapeR Version: 1.32.0 Depends: R (>= 3.4), GenomicRanges Imports: Rcpp (>= 0.12.1), Biostrings, fields LinkingTo: Rcpp Suggests: AnnotationHub, knitr, rmarkdown, testthat, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19, caret License: GPL-2 Archs: x64 Package: DominoEffect Version: 1.24.0 Depends: R(>= 3.5) Imports: biomaRt, data.table, utils, stats, Biostrings, pwalign, SummarizedExperiment, VariantAnnotation, AnnotationDbi, GenomeInfoDb, IRanges, GenomicRanges, methods Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) Package: doppelgangR Version: 1.32.0 Depends: R (>= 3.5.0), Biobase, BiocParallel Imports: sva, impute, digest, mnormt, methods, grDevices, graphics, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat License: GPL (>= 2.0) Package: Doscheda Version: 1.26.0 Depends: R (>= 3.4) Imports: methods, drc, stats, httr, jsonlite, reshape2 , vsn, affy, limma, stringr, ggplot2, graphics, grDevices, calibrate, corrgram, gridExtra, DT, shiny, shinydashboard, readxl, prodlim, matrixStats Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 Package: DOSE Version: 3.30.1 Depends: R (>= 3.5.0) Imports: AnnotationDbi, HDO.db, BiocParallel, fgsea, ggplot2, GOSemSim (>= 2.27.1), methods, qvalue, reshape2, stats, utils, yulab.utils Suggests: prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, rmarkdown, org.Hs.eg.db, HPO.db, MPO.db, testthat License: Artistic-2.0 Package: doseR Version: 1.20.0 Depends: R (>= 3.6) Imports: edgeR, methods, stats, graphics, matrixStats, mclust, lme4, RUnit, SummarizedExperiment, digest, S4Vectors Suggests: BiocStyle, knitr, rmarkdown License: GPL Package: doubletrouble Version: 1.4.0 Depends: R (>= 4.2.0) Imports: syntenet, GenomicRanges, Biostrings, mclust, MSA2dist (>= 1.1.5), ggplot2, rlang, stats, utils, AnnotationDbi, GenomicFeatures, BiocParallel Suggests: txdbmaker, testthat (>= 3.0.0), knitr, feature, patchwork, BiocStyle, rmarkdown, covr, sessioninfo License: GPL-3 Package: dpeak Version: 1.16.0 Depends: R (>= 4.0.0), methods, stats, utils, graphics, Rcpp Imports: MASS, IRanges, BSgenome, grDevices, parallel LinkingTo: Rcpp Suggests: BSgenome.Ecoli.NCBI.20080805 License: GPL (>= 2) Archs: x64 Package: drawProteins Version: 1.24.0 Depends: R (>= 4.0) Imports: ggplot2, httr, dplyr, readr, tidyr Suggests: covr, testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE Package: dreamlet Version: 1.2.1 Depends: R (>= 4.3.0), variancePartition (>= 1.33.11), SingleCellExperiment, ggplot2 Imports: edgeR, SummarizedExperiment, DelayedMatrixStats, sparseMatrixStats, MatrixGenerics, Matrix, methods, purrr, GSEABase, data.table, zenith (>= 1.1.2), mashr (>= 0.2.52), ashr, dplyr, BiocParallel, ggbeeswarm, S4Vectors, IRanges, irlba, limma, metafor, remaCor, broom, tidyr, rlang, BiocGenerics, DelayedArray, gtools, reshape2, ggrepel, scattermore, Rcpp, lme4 (>= 1.1-33), MASS, Rdpack, utils, stats LinkingTo: Rcpp, beachmat Suggests: BiocStyle, knitr, pander, rmarkdown, muscat, ExperimentHub, RUnit, scater, scuttle License: Artistic-2.0 Archs: x64 Package: DRIMSeq Version: 1.32.0 Depends: R (>= 3.4.0) Imports: utils, stats, MASS, GenomicRanges, IRanges, S4Vectors, BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2, reshape2 Suggests: PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat License: GPL (>= 3) Package: DriverNet Version: 1.44.0 Depends: R (>= 2.10), methods License: GPL-3 Package: DropletUtils Version: 1.24.0 Depends: SingleCellExperiment Imports: utils, stats, methods, Matrix, Rcpp, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, BiocParallel, DelayedArray, DelayedMatrixStats, HDF5Array, rhdf5, edgeR, R.utils, dqrng, beachmat, scuttle LinkingTo: Rcpp, beachmat, Rhdf5lib, BH, dqrng, scuttle Suggests: testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles License: GPL-3 Archs: x64 Package: drugTargetInteractions Version: 1.12.0 Depends: methods, R (>= 4.1) Imports: utils, RSQLite, UniProt.ws, biomaRt,ensembldb, BiocFileCache,dplyr,rappdirs, AnnotationFilter, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, ggplot2, reshape2, DT, EnsDb.Hsapiens.v86 License: Artistic-2.0 Package: DrugVsDisease Version: 2.46.0 Depends: R (>= 2.10), affy, limma, biomaRt, ArrayExpress, GEOquery, DrugVsDiseasedata, cMap2data, qvalue Imports: annotate, hgu133a.db, hgu133a2.db, hgu133plus2.db, RUnit, BiocGenerics, xtable License: GPL-3 Package: DSS Version: 2.52.0 Depends: R (>= 3.5.0), methods, Biobase, BiocParallel, bsseq, parallel Imports: utils, graphics, stats, splines Suggests: BiocStyle, knitr, rmarkdown, edgeR License: GPL Archs: x64 Package: dStruct Version: 1.10.0 Depends: R (>= 4.1) Imports: zoo, ggplot2, purrr, reshape2, parallel, IRanges, S4Vectors, rlang, grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown, tidyverse, testthat (>= 3.0.0) License: GPL (>= 2) Package: DTA Version: 2.50.0 Depends: R (>= 2.10), LSD Imports: scatterplot3d License: Artistic-2.0 Package: Dune Version: 1.16.0 Depends: R (>= 3.6) Imports: BiocParallel, SummarizedExperiment, utils, ggplot2, dplyr, tidyr, RColorBrewer, magrittr, gganimate, purrr, aricode Suggests: knitr, rmarkdown, testthat (>= 2.1.0) License: MIT + file LICENSE Package: dyebias Version: 1.64.0 Depends: R (>= 1.4.1), marray, Biobase Suggests: limma, convert, GEOquery, dyebiasexamples, methods License: GPL-3 Package: DynDoc Version: 1.82.0 Depends: methods, utils Imports: methods License: Artistic-2.0 Package: easier Version: 1.10.0 Depends: R (>= 4.2.0) Imports: progeny, easierData, dorothea (>= 1.6.0), decoupleR, quantiseqr, ROCR, grDevices, stats, graphics, ggplot2, ggpubr, DESeq2, utils, dplyr, tidyr, tibble, matrixStats, rlang, BiocParallel, reshape2, rstatix, ggrepel, magrittr, coin Suggests: knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment, viper License: MIT + file LICENSE Package: EasyCellType Version: 1.6.0 Depends: R (>= 4.2.0) Imports: clusterProfiler, dplyr, forcats, ggplot2, magrittr, rlang, stats, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, vctrs (>= 0.6.4), BiocStyle Suggests: knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager, devtools, BiocStyle License: Artistic-2.0 Package: easylift Version: 1.2.0 Depends: GenomicRanges, BiocFileCache Imports: rtracklayer, GenomeInfoDb, R.utils, tools, methods Suggests: testthat (>= 3.0.0), IRanges, knitr, BiocStyle, rmarkdown License: MIT + file LICENSE Package: easyreporting Version: 1.16.0 Depends: R (>= 3.5.0) Imports: rmarkdown, methods, tools, shiny, rlang Suggests: distill, BiocStyle, knitr, readxl, edgeR, limma, EDASeq, statmod License: Artistic-2.0 Package: easyRNASeq Version: 2.39.0 Imports: Biobase (>= 2.50.0), BiocFileCache (>= 1.14.0), BiocGenerics (>= 0.36.0), BiocParallel (>= 1.24.1), biomaRt (>= 2.46.0), Biostrings (>= 2.58.0), edgeR (>= 3.32.0), GenomeInfoDb (>= 1.26.0), genomeIntervals (>= 1.46.0), GenomicAlignments (>= 1.26.0), GenomicRanges (>= 1.42.0), SummarizedExperiment (>= 1.20.0), graphics, IRanges (>= 2.24.0), LSD (>= 4.1-0), locfit, methods, parallel, rappdirs (>= 0.3.1), Rsamtools (>= 2.6.0), S4Vectors (>= 0.28.0), ShortRead (>= 1.48.0), utils Suggests: BiocStyle (>= 2.18.0), BSgenome (>= 1.58.0), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.32) License: Artistic-2.0 Package: EBarrays Version: 2.68.0 Depends: R (>= 1.8.0), Biobase, lattice, methods Imports: Biobase, cluster, graphics, grDevices, lattice, methods, stats License: GPL (>= 2) Archs: x64 Package: EBcoexpress Version: 1.48.0 Depends: EBarrays, mclust, minqa Suggests: graph, igraph, colorspace License: GPL (>= 2) Archs: x64 Package: EBImage Version: 4.46.0 Depends: methods Imports: BiocGenerics (>= 0.7.1), graphics, grDevices, stats, abind, tiff, jpeg, png, locfit, fftwtools (>= 0.9-7), utils, htmltools, htmlwidgets, RCurl Suggests: BiocStyle, digest, knitr, rmarkdown, shiny License: LGPL Archs: x64 Package: EBSEA Version: 1.32.0 Depends: R (>= 4.0.0) Imports: DESeq2, graphics, stats, EmpiricalBrownsMethod Suggests: knitr, rmarkdown License: GPL-2 Package: EBSeq Version: 2.2.0 Depends: blockmodeling, gplots, testthat, R (>= 3.0.0) Imports: Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0) LinkingTo: Rcpp,RcppEigen,BH License: Artistic-2.0 Archs: x64 Package: ecolitk Version: 1.76.0 Depends: R (>= 2.10) Imports: Biobase, graphics, methods Suggests: ecoliLeucine, ecolicdf, graph, multtest, affy License: GPL (>= 2) Package: EDASeq Version: 2.38.0 Depends: Biobase (>= 2.15.1), ShortRead (>= 1.11.42) Imports: methods, graphics, BiocGenerics, IRanges (>= 1.13.9), aroma.light, Rsamtools (>= 1.5.75), biomaRt, Biostrings, AnnotationDbi, GenomicFeatures, GenomicRanges, BiocManager Suggests: BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat, DESeq2, rmarkdown License: Artistic-2.0 Package: edge Version: 2.36.0 Depends: R(>= 3.1.0), Biobase Imports: methods, splines, sva, qvalue(>= 1.99.0), MASS Suggests: testthat, knitr, ggplot2, reshape2 License: MIT + file LICENSE Archs: x64 Package: edgeR Version: 4.2.0 Depends: R (>= 3.6.0), limma (>= 3.41.5) Imports: methods, graphics, stats, utils, locfit, Rcpp LinkingTo: Rcpp Suggests: jsonlite, readr, rhdf5, splines, knitr, AnnotationDbi, Biobase, BiocStyle, SummarizedExperiment, org.Hs.eg.db, Matrix, SeuratObject License: GPL (>= 2) Archs: x64 Package: EDIRquery Version: 1.4.0 Depends: R (>= 4.2.0) Imports: tibble (>= 3.1.6), tictoc (>= 1.0.1), utils (>= 4.1.3), stats (>= 4.1.3), readr (>= 2.1.2), InteractionSet (>= 1.22.0), GenomicRanges (>= 1.46.1) Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 Package: eds Version: 1.6.0 Depends: Matrix Imports: Rcpp LinkingTo: Rcpp Suggests: knitr, tximportData, testthat (>= 3.0.0) License: GPL-2 Archs: x64 Package: eegc Version: 1.30.0 Depends: R (>= 3.4.0) Imports: R.utils, gplots, sna, wordcloud, igraph, pheatmap, edgeR, DESeq2, clusterProfiler, S4Vectors, ggplot2, org.Hs.eg.db, org.Mm.eg.db, limma, DOSE, AnnotationDbi Suggests: knitr License: GPL-2 Package: EGAD Version: 1.32.0 Depends: R(>= 3.5) Imports: gplots, Biobase, GEOquery, limma, impute, RColorBrewer, zoo, igraph, plyr, MASS, RCurl, methods Suggests: knitr, testthat, rmarkdown, markdown License: GPL-2 Package: EGSEA Version: 1.32.0 Depends: R (>= 4.3.0), Biobase, gage (>= 2.14.4), AnnotationDbi, topGO (>= 2.16.0), pathview (>= 1.4.2) Imports: PADOG (>= 1.6.0), GSVA (>= 1.12.0), globaltest (>= 5.18.0), limma (>= 3.20.9), edgeR (>= 3.6.8), HTMLUtils (>= 0.1.5), hwriter (>= 1.2.2), gplots (>= 2.14.2), ggplot2 (>= 1.0.0), safe (>= 3.4.0), stringi (>= 0.5.0), parallel, stats, metap, grDevices, graphics, utils, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, RColorBrewer, methods, EGSEAdata (>= 1.3.1), htmlwidgets, plotly, DT Suggests: BiocStyle, knitr, testthat License: GPL-3 Package: eiR Version: 1.44.0 Depends: R (>= 2.10.0), ChemmineR (>= 2.15.15), methods, DBI Imports: snow, tools, snowfall, RUnit, methods, ChemmineR, RCurl, digest, BiocGenerics, RcppAnnoy (>= 0.0.9) Suggests: BiocStyle, knitcitations, knitr, knitrBootstrap,rmarkdown,RSQLite License: Artistic-2.0 Archs: x64 Package: eisaR Version: 1.16.0 Depends: R (>= 4.1) Imports: graphics, stats, GenomicRanges, S4Vectors, IRanges, limma, edgeR (>= 4.0), methods, SummarizedExperiment, BiocGenerics, utils Suggests: knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie, Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38, ensembldb, AnnotationDbi, GenomicFeatures, txdbmaker, rtracklayer License: GPL-3 Package: ELMER Version: 2.28.0 Depends: R (>= 3.4.0), ELMER.data (>= 2.9.3) Imports: GenomicRanges, ggplot2, reshape, grid, grDevices, graphics, methods, parallel, stats, utils, IRanges, GenomeInfoDb, S4Vectors, GenomicFeatures, TCGAbiolinks (>= 2.23.7), plyr, Matrix, dplyr, Gviz, ComplexHeatmap, circlize, MultiAssayExperiment, SummarizedExperiment, biomaRt, doParallel, downloader, ggrepel, lattice, magrittr, readr, scales, rvest, xml2, plotly, gridExtra, rmarkdown, stringr, tibble, tidyr, progress, purrr, reshape2, ggpubr, rtracklayer (>= 1.61.2), DelayedArray Suggests: BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr, sesameData License: GPL-3 Package: EMDomics Version: 2.34.0 Depends: R (>= 3.2.1) Imports: emdist, BiocParallel, matrixStats, ggplot2, CDFt, preprocessCore Suggests: knitr License: MIT + file LICENSE Package: EmpiricalBrownsMethod Version: 1.32.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE Package: EnhancedVolcano Version: 1.22.0 Depends: ggplot2, ggrepel Imports: methods Suggests: ggalt, ggrastr, RUnit, BiocGenerics, knitr, DESeq2, pasilla, airway, org.Hs.eg.db, gridExtra, magrittr, rmarkdown License: GPL-3 Package: enhancerHomologSearch Version: 1.10.0 Depends: R (>= 4.1.0), methods Imports: BiocGenerics, Biostrings, BSgenome, BiocParallel, BiocFileCache, GenomeInfoDb, GenomicRanges, httr, IRanges, jsonlite, motifmatchr, Matrix, pwalign, rtracklayer, Rcpp, S4Vectors, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, MotifDb, testthat, TFBSTools License: GPL (>= 2) Archs: x64 Package: EnMCB Version: 1.16.0 Depends: R (>= 4.0) Imports: survivalROC, glmnet, rms, mboost, Matrix, igraph, methods, survivalsvm, ggplot2, boot, e1071, survival, BiocFileCache Suggests: SummarizedExperiment, testthat, Biobase, survminer, affycoretools, knitr, plotROC, limma, rmarkdown License: GPL-2 Package: ENmix Version: 1.40.2 Depends: parallel,doParallel,foreach,SummarizedExperiment,stats,R (>= 3.5.0) Imports: grDevices,graphics,matrixStats,methods,utils,irlba, geneplotter,impute,minfi,RPMM,illuminaio,dynamicTreeCut,IRanges,gtools, Biobase,ExperimentHub,AnnotationHub,genefilter,gplots,quadprog,S4Vectors Suggests: minfiData, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 Package: EnrichedHeatmap Version: 1.34.0 Depends: R (>= 3.6.0), methods, grid, ComplexHeatmap (>= 2.11.0), GenomicRanges Imports: matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize (>= 0.4.5), IRanges LinkingTo: Rcpp Suggests: testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter, RColorBrewer License: MIT + file LICENSE Archs: x64 Package: EnrichmentBrowser Version: 2.34.1 Depends: SummarizedExperiment, graph Imports: AnnotationDbi, BiocFileCache, BiocManager, GSEABase, GO.db, KEGGREST, KEGGgraph, Rgraphviz, S4Vectors, SPIA, edgeR, graphite, hwriter, limma, methods, pathview, safe Suggests: ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools, airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr, rmarkdown, statmod License: Artistic-2.0 Package: enrichplot Version: 1.24.0 Depends: R (>= 3.5.0) Imports: aplot (>= 0.2.1), DOSE (>= 3.16.0), ggfun (>= 0.1.3), ggnewscale, ggplot2, ggraph, graphics, grid, igraph, methods, plyr, purrr, RColorBrewer, reshape2, rlang, stats, utils, scatterpie, shadowtext, GOSemSim, magrittr, ggtree, yulab.utils (>= 0.0.8) Suggests: clusterProfiler, dplyr, europepmc, ggupset, knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, AnnotationDbi, ggplotify, ggridges, grDevices, gridExtra, ggrepel (>= 0.9.0), ggstar, scales, ggtreeExtra, tidydr License: Artistic-2.0 Package: enrichTF Version: 1.20.0 Depends: pipeFrame Imports: BSgenome, rtracklayer, motifmatchr, TFBSTools, R.utils, methods, JASPAR2018, GenomeInfoDb, GenomicRanges, IRanges, BiocGenerics, S4Vectors, utils, parallel, stats, ggpubr, heatmap3, ggplot2, clusterProfiler, rmarkdown, grDevices, magrittr Suggests: knitr, testthat, webshot License: GPL-3 Package: enrichViewNet Version: 1.2.0 Depends: R (>= 4.2.0) Imports: gprofiler2, strex, RCy3, jsonlite, stringr, enrichplot, DOSE, methods Suggests: BiocStyle, knitr, rmarkdown, ggplot2, testthat License: Artistic-2.0 Package: ensembldb Version: 2.28.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.31.18), GenomicFeatures (>= 1.49.6), AnnotationFilter (>= 1.5.2) Imports: methods, RSQLite (>= 1.1), DBI, Biobase, GenomeInfoDb, AnnotationDbi (>= 1.31.19), rtracklayer, S4Vectors (>= 0.23.10), Rsamtools, IRanges (>= 2.13.24), ProtGenerics, Biostrings (>= 2.47.9), curl Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), rmarkdown, AnnotationHub Enhances: RMariaDB, shiny License: LGPL Package: epialleleR Version: 1.12.0 Depends: R (>= 4.1) Imports: stats, methods, utils, GenomicRanges, BiocGenerics, GenomeInfoDb, SummarizedExperiment, VariantAnnotation, data.table, Rcpp LinkingTo: Rcpp, BH, Rhtslib, zlibbioc Suggests: RUnit, knitr, rmarkdown, ggplot2, ggstance, gridExtra License: Artistic-2.0 Archs: x64 Package: epidecodeR Version: 1.12.0 Depends: R (>= 3.1.0) Imports: EnvStats, ggplot2, rtracklayer, GenomicRanges, IRanges, rstatix, ggpubr, methods, stats, utils, dplyr Suggests: knitr, rmarkdown License: GPL-3 Package: EpiDISH Version: 2.20.0 Depends: R (>= 4.1) Imports: MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr, Matrix Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat License: GPL-2 Package: epigenomix Version: 1.44.0 Depends: R (>= 3.5.0), methods, Biobase, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment Imports: BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb, beadarray License: LGPL-3 Package: epigraHMM Version: 1.12.0 Depends: R (>= 3.5.0) Imports: Rcpp, magrittr, data.table, SummarizedExperiment, methods, GenomeInfoDb, GenomicRanges, rtracklayer, IRanges, Rsamtools, bamsignals, csaw, S4Vectors, limma, stats, Rhdf5lib, rhdf5, Matrix, MASS, scales, ggpubr, ggplot2, GreyListChIP, pheatmap, grDevices LinkingTo: Rcpp, RcppArmadillo, Rhdf5lib Suggests: testthat, knitr, rmarkdown, BiocStyle, BSgenome.Rnorvegicus.UCSC.rn4, gcapc, chromstaRData License: MIT + file LICENSE Archs: x64 Package: EpiMix Version: 1.6.1 Depends: R (>= 4.2.0), EpiMix.data (>= 1.2.2) Imports: AnnotationHub, AnnotationDbi, Biobase, biomaRt, data.table, doParallel, doSNOW, downloader, dplyr, ELMER.data, ExperimentHub, foreach, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, impute, IRanges, limma, methods, parallel, plyr, progress, R.matlab, RColorBrewer, RCurl, rlang, RPMM, S4Vectors, stats, SummarizedExperiment, tibble, tidyr, utils Suggests: BiocStyle, clusterProfiler, DT, GEOquery, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, multiMiR, miRBaseConverter License: GPL-3 Package: epimutacions Version: 1.8.0 Depends: R (>= 4.3.0), epimutacionsData Imports: minfi, bumphunter, isotree, robustbase, ggplot2, GenomicRanges, GenomicFeatures, IRanges, SummarizedExperiment, stats, matrixStats, BiocGenerics, S4Vectors, utils, biomaRt, BiocParallel, GenomeInfoDb, Homo.sapiens, purrr, tibble, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, rtracklayer, AnnotationDbi, AnnotationHub, ExperimentHub, reshape2, grid, ensembldb, gridExtra, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, ggrepel Suggests: testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra, methods, grDevices License: MIT + file LICENSE Archs: x64 Package: epiNEM Version: 1.28.0 Depends: R (>= 4.1) Imports: BoolNet, e1071, gtools, stats, igraph, utils, lattice, latticeExtra, RColorBrewer, pcalg, minet, grDevices, graph, mnem, latex2exp Suggests: knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db, BiocStyle License: GPL-3 Package: epiregulon Version: 1.0.1 Depends: R (>= 4.4), SingleCellExperiment Imports: AnnotationHub, BiocParallel, ExperimentHub, Matrix, Rcpp, S4Vectors, SummarizedExperiment, bluster, checkmate, entropy, lifecycle, methods, scran, scuttle, stats, utils, scMultiome, GenomeInfoDb, GenomicRanges, AUCell, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, motifmatchr, IRanges, beachmat LinkingTo: Rcpp, beachmat Suggests: knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), coin, scater License: MIT + file LICENSE Archs: x64 Package: epiregulon.extra Version: 1.0.0 Depends: R (>= 4.4), SingleCellExperiment Imports: scran, ComplexHeatmap, Matrix, SummarizedExperiment, checkmate, circlize, clusterProfiler, ggplot2, ggraph, igraph, lifecycle, patchwork, reshape2, scales, scater, stats Suggests: epiregulon, knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), EnrichmentBrowser, msigdbr, dorothea, scMultiome, S4Vectors, scuttle, vdiffr, ggrastr, ggrepel License: MIT + file LICENSE Package: epistack Version: 1.10.0 Depends: R (>= 4.1) Imports: GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors, IRanges, graphics, plotrix, grDevices, stats, methods Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick License: MIT + file LICENSE Package: epistasisGA Version: 1.6.0 Depends: R (>= 4.2) Imports: BiocParallel, data.table, matrixStats, stats, survival, igraph, batchtools, qgraph, grDevices, parallel, ggplot2, grid, bigmemory, graphics, utils LinkingTo: Rcpp, RcppArmadillo, BH, bigmemory Suggests: BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat (>= 3.0.0) License: GPL-3 Archs: x64 Package: EpiTxDb Version: 1.16.0 Depends: R (>= 4.0), AnnotationDbi, Modstrings Imports: methods, utils, httr, xml2, curl, rex, GenomicFeatures, txdbmaker, GenomicRanges, GenomeInfoDb, BiocGenerics, BiocFileCache, S4Vectors, IRanges, RSQLite, DBI, Biostrings, tRNAdbImport Suggests: BiocStyle, knitr, rmarkdown, testthat, httptest, AnnotationHub, ensembldb, ggplot2, EpiTxDb.Hs.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Scerevisiae.UCSC.sacCer3, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 Package: epivizr Version: 2.34.0 Depends: R (>= 3.5.0), methods Imports: epivizrServer (>= 1.1.1), epivizrData (>= 1.3.4), GenomicRanges, S4Vectors, IRanges, bumphunter, GenomeInfoDb Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, minfi, rmarkdown License: Artistic-2.0 Package: epivizrChart Version: 1.26.0 Depends: R (>= 3.5.0) Imports: epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson, methods, BiocGenerics Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub License: Artistic-2.0 Package: epivizrData Version: 1.32.0 Depends: R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase Imports: S4Vectors, GenomicRanges, SummarizedExperiment (>= 0.2.0), OrganismDbi, GenomicFeatures, GenomeInfoDb, IRanges, ensembldb Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI, matrixStats License: MIT + file LICENSE Package: epivizrServer Version: 1.32.0 Depends: R (>= 3.2.3), methods Imports: httpuv (>= 1.3.0), R6 (>= 2.0.0), rjson, mime (>= 0.2) Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE Package: epivizrStandalone Version: 1.32.0 Depends: R (>= 3.2.3), epivizr (>= 2.3.6), methods Imports: git2r, epivizrServer, GenomeInfoDb, BiocGenerics, GenomicFeatures, S4Vectors Suggests: testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9), Mus.musculus, Biobase, BiocStyle License: MIT + file LICENSE Package: erccdashboard Version: 1.38.0 Depends: R (>= 3.2), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0) Imports: edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr, qvalue, reshape2, ROCR, scales, stringr License: GPL (>= 2) Package: erma Version: 1.20.0 Depends: R (>= 3.1), methods, Homo.sapiens, GenomicFiles (>= 1.5.2) Imports: rtracklayer (>= 1.38.1), S4Vectors (>= 0.23.18), BiocGenerics, GenomicRanges, SummarizedExperiment, ggplot2, GenomeInfoDb, Biobase, shiny, BiocParallel, IRanges, AnnotationDbi Suggests: rmarkdown, BiocStyle, knitr, GO.db, png, DT, doParallel License: Artistic-2.0 Package: ERSSA Version: 1.22.0 Depends: R (>= 4.0.0) Imports: edgeR (>= 3.23.3), DESeq2 (>= 1.21.16), ggplot2 (>= 3.0.0), RColorBrewer (>= 1.1-2), plyr (>= 1.8.4), BiocParallel (>= 1.15.8), apeglm (>= 1.4.2), grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 | file LICENSE Package: escape Version: 2.0.0 Depends: R (>= 4.1) Imports: AUCell, BiocParallel, grDevices, dplyr, ggdist, ggplot2, ggpointdensity, GSEABase, GSVA, SingleCellExperiment, ggridges, msigdbr, stats, reshape2, patchwork, MatrixGenerics, utils, SummarizedExperiment, UCell, stringr, methods, SeuratObject Suggests: Seurat, hexbin, scran, knitr, rmarkdown, markdown, BiocStyle, RColorBrewer, rlang, spelling, testthat (>= 3.0.0), vdiffr License: MIT + file LICENSE Package: escheR Version: 1.4.0 Depends: ggplot2, R (>= 4.3) Imports: SpatialExperiment (>= 1.6.1), SingleCellExperiment, rlang, SummarizedExperiment Suggests: STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle, ggpubr, scran, scater, scuttle, Seurat, hexbin License: MIT + file LICENSE Package: esetVis Version: 1.30.0 Imports: mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils, grDevices, methods Suggests: ggplot2, ggvis, plotly, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment, GO.db License: GPL-3 Package: eudysbiome Version: 1.34.0 Depends: R (>= 3.1.0) Imports: plyr, Rsamtools, R.utils, Biostrings License: GPL-2 Package: evaluomeR Version: 1.20.5 Depends: R (>= 3.6), SummarizedExperiment, MultiAssayExperiment, cluster (>= 2.0.9), fpc (>= 2.2-3), randomForest (>= 4.6.14), flexmix (>= 2.3.15), RSKC (>= 2.4.2), sparcl (>= 1.0.4) Imports: corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2, ggdendro, plotrix, stats, matrixStats, Rdpack, MASS, class, prabclus, mclust, kableExtra, dplyr, dendextend (>= 1.16.0) Suggests: BiocStyle, knitr, rmarkdown, magrittr License: GPL-3 Package: EventPointer Version: 3.12.0 Depends: R (>= 3.5.0), SGSeq, Matrix, SummarizedExperiment Imports: GenomicFeatures, stringr, GenomeInfoDb, igraph, MASS, nnls, limma, matrixStats, RBGL, prodlim, graph, methods, utils, stats, doParallel, foreach, affxparser, GenomicRanges, S4Vectors, IRanges, qvalue, cobs, rhdf5, BSgenome, Biostrings, glmnet, abind, iterators, lpSolve, poibin, speedglm, tximport, fgsea Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra License: Artistic-2.0 Archs: x64 Package: EWCE Version: 1.12.0 Depends: R (>= 4.2), RNOmni (>= 1.0) Imports: stats, utils, methods, ewceData (>= 1.7.1), dplyr, ggplot2, reshape2, limma, stringr, HGNChelper, Matrix, parallel, SingleCellExperiment, SummarizedExperiment, DelayedArray, BiocParallel, orthogene (>= 0.99.8), data.table Suggests: rworkflows, remotes, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2, MAST, DelayedMatrixStats, ggdendro, scales, patchwork License: GPL-3 Package: ExiMiR Version: 2.46.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), affy (>= 1.26.1), limma Imports: affyio(>= 1.13.3), Biobase(>= 2.5.5), preprocessCore(>= 1.10.0) Suggests: mirna10cdf License: GPL-2 Package: exomePeak2 Version: 1.16.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: Rsamtools,GenomicAlignments,GenomicRanges,GenomicFeatures,DESeq2,ggplot2,mclust,BSgenome,Biostrings,GenomeInfoDb,BiocParallel,IRanges,S4Vectors,rtracklayer,methods,stats,utils,BiocGenerics,magrittr,speedglm,splines Suggests: knitr, rmarkdown License: Artistic-2.0 Package: ExperimentHub Version: 2.12.0 Depends: methods, BiocGenerics (>= 0.15.10), AnnotationHub (>= 3.3.6), BiocFileCache (>= 1.5.1) Imports: utils, S4Vectors, BiocManager, rappdirs Suggests: knitr, BiocStyle, rmarkdown, HubPub, GenomicAlignments Enhances: ExperimentHubData License: Artistic-2.0 Package: ExperimentHubData Version: 1.30.0 Depends: utils, BiocGenerics (>= 0.15.10), S4Vectors, AnnotationHubData (>= 1.21.3) Imports: methods, ExperimentHub, BiocManager, DBI, httr, curl Suggests: GenomeInfoDb, RUnit, knitr, BiocStyle, rmarkdown, HubPub License: Artistic-2.0 Package: ExperimentSubset Version: 1.14.0 Depends: R (>= 4.0.0), SummarizedExperiment, SingleCellExperiment, SpatialExperiment, TreeSummarizedExperiment Imports: methods, Matrix, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat, covr, stats, scran, scater, scds, TENxPBMCData, airway License: MIT + file LICENSE Package: ExploreModelMatrix Version: 1.16.0 Imports: shiny (>= 1.5.0), shinydashboard, DT, cowplot, utils, dplyr, magrittr, tidyr, ggplot2, stats, methods, rintrojs, scales, tibble, MASS, limma, S4Vectors, shinyjs Suggests: testthat (>= 2.1.0), knitr, rmarkdown, htmltools, BiocStyle License: MIT + file LICENSE Package: ExpressionAtlas Version: 1.32.0 Depends: R (>= 4.2.0), methods, Biobase, SummarizedExperiment, limma, S4Vectors, xml2, RCurl, jsonlite, BiocStyle Imports: utils, XML, httr Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) Package: extraChIPs Version: 1.8.1 Depends: BiocParallel, R (>= 4.2.0), GenomicRanges, ggplot2 (>= 3.5.0), ggside (>= 0.3.1), SummarizedExperiment, tibble Imports: BiocIO, broom, ComplexUpset, csaw, dplyr (>= 1.1.1), edgeR (>= 4.0), forcats, GenomeInfoDb, GenomicInteractions, ggforce, ggrepel, glue, grDevices, grid, InteractionSet, IRanges, matrixStats, methods, patchwork, RColorBrewer, rlang, Rsamtools, rtracklayer, S4Vectors, scales, stats, stringr, tidyr, tidyselect, utils, vctrs, VennDiagram Suggests: BiocStyle, covr, cqn, DESeq2, EnrichedHeatmap, Gviz, harmonicmeanp, here, knitr, limma, magrittr, plyranges, quantro, rmarkdown, testthat (>= 3.0.0), tidyverse License: GPL-3 Archs: x64 Package: fabia Version: 2.50.0 Depends: R (>= 3.6.0), Biobase Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) Archs: x64 Package: factDesign Version: 1.80.0 Depends: Biobase (>= 2.5.5) Imports: stats Suggests: affy, genefilter, multtest License: LGPL Package: factR Version: 1.6.0 Depends: R (>= 4.2) Imports: BiocGenerics (>= 0.46), Biostrings (>= 2.68), GenomeInfoDb (>= 1.36), dplyr (>= 1.1), GenomicFeatures (>= 1.52), GenomicRanges (>= 1.52), IRanges (>= 2.34), purrr (>= 1.0), rtracklayer (>= 1.60), tidyr (>= 1.3), methods (>= 4.3), BiocParallel (>= 1.34), S4Vectors (>= 0.38), data.table (>= 1.14), rlang (>= 1.1), tibble (>= 3.2), wiggleplotr (>= 1.24), RCurl (>= 1.98), XML (>= 3.99), drawProteins (>= 1.20), ggplot2 (>= 3.4), stringr (>= 1.5), pbapply (>= 1.7), stats (>= 4.3), utils (>= 4.3), graphics (>= 4.3), crayon (>= 1.5) Suggests: AnnotationHub (>= 2.22), BSgenome (>= 1.58), BSgenome.Mmusculus.UCSC.mm10, testthat, knitr, rmarkdown, markdown, zeallot, rmdformats, bio3d (>= 2.4), signalHsmm (>= 1.5), tidyverse (>= 1.3), covr, patchwork License: file LICENSE Package: faers Version: 1.0.3 Depends: R (>= 3.5.0) Imports: BiocParallel, brio, cli, curl (>= 5.0.0), data.table, httr2 (>= 1.0.0), MCMCpack, methods, openEBGM, rlang (>= 1.1.0), rvest, tools, utils, vroom, xml2 Suggests: BiocStyle, countrycode, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE Package: FamAgg Version: 1.32.0 Depends: methods, kinship2, igraph Imports: gap (>= 1.1-17), Matrix, BiocGenerics, utils, survey Suggests: BiocStyle, knitr, RUnit, rmarkdown License: MIT + file LICENSE Package: famat Version: 1.14.0 Depends: R (>= 4.0) Imports: KEGGREST, mgcv, stats, BiasedUrn, dplyr, gprofiler2, rWikiPathways, reactome.db, stringr, GO.db, ontologyIndex, tidyr, shiny, shinydashboard, shinyBS, plotly, magrittr, DT, clusterProfiler, org.Hs.eg.db Suggests: BiocStyle, knitr, rmarkdown, testthat, BiocManager License: GPL-3 Package: farms Version: 1.56.0 Depends: R (>= 2.8), affy (>= 1.20.0), MASS, methods Imports: affy, MASS, Biobase (>= 1.13.41), methods, graphics Suggests: affydata, Biobase, utils License: LGPL (>= 2.1) Package: fastLiquidAssociation Version: 1.40.0 Depends: methods, LiquidAssociation, parallel, doParallel, stats, Hmisc, utils Imports: WGCNA, impute, preprocessCore Suggests: GOstats, yeastCC, org.Sc.sgd.db License: GPL-2 Package: FastqCleaner Version: 1.22.0 Imports: methods, shiny, stats, IRanges, Biostrings, ShortRead, DT, S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12) LinkingTo: Rcpp Suggests: BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE Archs: x64 Package: fastreeR Version: 1.8.0 Depends: R (>= 4.4) Imports: ape, data.table, dynamicTreeCut, methods, R.utils, rJava, stats, stringr, utils Suggests: BiocFileCache, BiocStyle, graphics, knitr, memuse, rmarkdown, spelling, testthat (>= 3.0.0) License: GPL-3 Package: fastseg Version: 1.50.0 Depends: R (>= 2.13), GenomicRanges, Biobase Imports: methods, graphics, grDevices, stats, BiocGenerics, S4Vectors, IRanges Suggests: DNAcopy, oligo, BiocStyle, knitr License: LGPL (>= 2.0) Archs: x64 Package: FCBF Version: 2.12.0 Depends: R (>= 4.1) Imports: ggplot2, gridExtra, pbapply, parallel, SummarizedExperiment, stats, mclust Suggests: caret, mlbench, SingleCellExperiment, knitr, rmarkdown, testthat, BiocManager License: MIT + file LICENSE Package: fCCAC Version: 1.30.0 Depends: R (>= 4.2.0), S4Vectors, IRanges, GenomicRanges, grid Imports: fda, RColorBrewer, genomation, ggplot2, ComplexHeatmap, grDevices, stats, utils Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 Package: fCI Version: 1.34.0 Depends: R (>= 3.1),FNN, psych, gtools, zoo, rgl, grid, VennDiagram Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) Package: fcScan Version: 1.18.0 Imports: stats, plyr, VariantAnnotation, SummarizedExperiment, rtracklayer, GenomicRanges, methods, IRanges, foreach, doParallel, parallel Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 Package: fdrame Version: 1.76.0 Imports: tcltk, graphics, grDevices, stats, utils License: GPL (>= 2) Archs: x64 Package: FEAST Version: 1.12.0 Depends: R (>= 4.1), mclust, BiocParallel, SummarizedExperiment Imports: SingleCellExperiment, methods, stats, utils, irlba, TSCAN, SC3, matrixStats Suggests: rmarkdown, Seurat, ggpubr, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-2 Archs: x64 Package: FeatSeekR Version: 1.4.0 Imports: pheatmap, MASS, pracma, stats, SummarizedExperiment, methods Suggests: rmarkdown, knitr, BiocStyle, DmelSGI, testthat (>= 3.0.0) License: GPL-3 Package: fedup Version: 1.12.0 Depends: R (>= 4.1) Imports: openxlsx, tibble, dplyr, data.table, ggplot2, ggthemes, forcats, RColorBrewer, RCy3, utils, stats Suggests: biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr License: MIT + file LICENSE Package: FELLA Version: 1.24.0 Depends: R (>= 3.5.0) Imports: methods, igraph, Matrix, KEGGREST, plyr, stats, graphics, utils Suggests: shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown, testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, GOSemSim License: GPL-3 Package: fenr Version: 1.2.1 Depends: R (>= 4.1.0) Imports: tools, methods, assertthat, rlang, dplyr, tidyr, tidyselect, tibble, purrr, readr, stringr, httr2, rvest, progress, BiocFileCache, shiny, ggplot2 Suggests: BiocStyle, testthat, knitr, rmarkdown, topGO License: MIT + file LICENSE Package: ffpe Version: 1.48.0 Depends: R (>= 2.10.0), TTR, methods Imports: Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc Suggests: genefilter, ffpeExampleData License: GPL (> 2) Package: fgga Version: 1.12.0 Depends: R (>= 4.3), RBGL Imports: graph, stats, e1071, methods, gRbase, jsonlite, BiocFileCache, curl, igraph Suggests: knitr, rmarkdown, GOstats, GO.db, BiocGenerics, pROC, RUnit, BiocStyle License: GPL-3 Package: FGNet Version: 3.38.0 Depends: R (>= 4.2.0) Imports: igraph (>= 0.6), hwriter, R.utils, XML, plotrix, reshape2, RColorBrewer, png, methods, stats, utils, graphics, grDevices Suggests: RCurl, gage, topGO, GO.db, reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, BiocManager License: GPL (>= 2) Package: fgsea Version: 1.30.0 Depends: R (>= 4.1) Imports: Rcpp, data.table, BiocParallel, stats, ggplot2 (>= 2.2.0), cowplot, grid, fastmatch, Matrix, scales, utils LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery, msigdbr, aggregation, Seurat License: MIT + file LICENCE Archs: x64 Package: FilterFFPE Version: 1.14.0 Imports: foreach, doParallel, GenomicRanges, IRanges, Rsamtools, parallel, S4Vectors Suggests: BiocStyle License: LGPL-3 Package: findIPs Version: 1.0.0 Depends: graphics, R (>= 4.4.0) Imports: Biobase, BiocParallel, parallel, stats, SummarizedExperiment, survival, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 Package: FindIT2 Version: 1.10.0 Depends: GenomicRanges, R (>= 3.5.0) Imports: withr, BiocGenerics, GenomeInfoDb, rtracklayer, S4Vectors, GenomicFeatures, dplyr, rlang, patchwork, ggplot2, BiocParallel, qvalue, stringr, utils, stats, ggrepel, tibble, tidyr, SummarizedExperiment, MultiAssayExperiment, IRanges, progress, purrr, glmnet, methods Suggests: BiocStyle, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), TxDb.Athaliana.BioMart.plantsmart28 License: Artistic-2.0 Package: FISHalyseR Version: 1.38.0 Depends: EBImage,abind Suggests: knitr License: Artistic-2.0 Package: fishpond Version: 2.10.0 Imports: graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, IRanges, SummarizedExperiment, GenomicRanges, matrixStats, svMisc, Matrix, SingleCellExperiment, jsonlite Suggests: testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, samr, DESeq2, apeglm, tximportData, limma, ensembldb, EnsDb.Hsapiens.v86, GenomicFeatures, AnnotationDbi, pheatmap, Gviz, GenomeInfoDb, data.table License: GPL-2 Package: FitHiC Version: 1.30.0 Imports: data.table, fdrtool, grDevices, graphics, Rcpp, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: GPL (>= 2) Archs: x64 Package: flagme Version: 1.60.0 Depends: gcspikelite, xcms, CAMERA Imports: gplots, graphics, MASS, methods, SparseM, stats, utils License: LGPL (>= 2) Archs: x64 Package: flowAI Version: 1.34.0 Depends: R (>= 3.6) Imports: ggplot2, flowCore, plyr, changepoint, knitr, reshape2, RColorBrewer, scales, methods, graphics, stats, utils, rmarkdown Suggests: testthat, shiny, BiocStyle License: GPL (>= 2) Package: flowBeads Version: 1.42.0 Depends: R (>= 2.15.0), methods, Biobase, rrcov, flowCore Imports: flowCore, rrcov, knitr, xtable Suggests: flowViz License: Artistic-2.0 Package: flowBin Version: 1.40.0 Depends: methods, flowCore, flowFP, R (>= 2.10) Imports: class, limma, snow, BiocGenerics Suggests: parallel License: Artistic-2.0 Package: flowcatchR Version: 1.38.0 Depends: R (>= 2.10), methods, EBImage Imports: colorRamps, abind, BiocParallel, graphics, stats, utils, plotly, shiny Suggests: BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE Package: flowCHIC Version: 1.38.0 Depends: R (>= 3.1.0) Imports: methods, flowCore, EBImage, vegan, hexbin, ggplot2, grid License: GPL-2 Package: flowClean Version: 1.42.0 Depends: R (>= 2.15.0), flowCore Imports: bit, changepoint, sfsmisc Suggests: flowViz, grid, gridExtra License: Artistic-2.0 Package: flowClust Version: 3.42.0 Depends: R(>= 2.5.0) Imports: BiocGenerics, methods, Biobase, graph, flowCore, parallel Suggests: testthat, flowWorkspace, flowWorkspaceData, knitr, rmarkdown, openCyto, flowStats(>= 4.7.1) License: MIT Archs: x64 Package: flowCore Version: 2.16.0 Depends: R (>= 3.5.0) Imports: Biobase, BiocGenerics (>= 0.29.2), grDevices, graphics, methods, stats, utils, stats4, Rcpp, matrixStats, cytolib (>= 2.13.1), S4Vectors LinkingTo: cpp11, BH(>= 1.81.0.0), cytolib, RProtoBufLib Suggests: Rgraphviz, flowViz, flowStats (>= 3.43.4), testthat, flowWorkspace, flowWorkspaceData, openCyto, knitr, ggcyto, gridExtra License: Artistic-2.0 Archs: x64 Package: flowCut Version: 1.14.0 Depends: R (>= 3.4), flowCore Imports: flowDensity (>= 1.13.1), Cairo, e1071, grDevices, graphics, stats,methods Suggests: RUnit, BiocGenerics, knitr, markdown, rmarkdown License: Artistic-2.0 Package: flowCyBar Version: 1.40.0 Depends: R (>= 3.0.0) Imports: gplots, vegan, methods License: GPL-2 Package: flowDensity Version: 1.38.0 Imports: flowCore, graphics, flowViz (>= 1.42), car, polyclip, gplots, methods, stats, grDevices Suggests: knitr,rmarkdown License: Artistic-2.0 Package: flowFP Version: 1.62.0 Depends: R (>= 2.10), flowCore, flowViz Imports: Biobase, BiocGenerics (>= 0.1.6), graphics, grDevices, methods, stats, stats4 Suggests: RUnit License: Artistic-2.0 Archs: x64 Package: flowGate Version: 1.4.0 Depends: flowWorkspace (>= 4.0.6), ggcyto (>= 1.16.0), R (>= 4.2) Imports: shiny (>= 1.5.0), BiocManager (>= 1.30.10), flowCore (>= 2.0.1), dplyr (>= 1.0.0), ggplot2 (>= 3.3.2), rlang (>= 0.4.7), purrr, tibble, methods Suggests: knitr, rmarkdown, stringr, tidyverse, testthat License: MIT + file LICENSE Package: flowGraph Version: 1.12.0 Depends: R (>= 4.1) Imports: effsize, furrr, future, purrr, ggiraph, ggrepel, ggplot2, igraph, Matrix, matrixStats, stats, utils, visNetwork, htmlwidgets, grDevices, methods, stringr, stringi, Rdpack, data.table (>= 1.9.5), gridExtra, Suggests: BiocStyle, dplyr, knitr, rmarkdown, testthat (>= 2.1.0) License: Artistic-2.0 Package: flowMap Version: 1.42.0 Depends: R (>= 3.0.1), ade4(>= 1.5-2), doParallel(>= 1.0.3), abind(>= 1.4.0), reshape2(>= 1.2.2), scales(>= 0.2.3), Matrix(>= 1.1-4), methods (>= 2.14) Suggests: BiocStyle, knitr License: GPL (>= 2) Package: flowMatch Version: 1.40.0 Depends: R (>= 3.0.0), Rcpp (>= 0.11.0), methods, flowCore Imports: Biobase LinkingTo: Rcpp Suggests: healthyFlowData License: Artistic-2.0 Archs: x64 Package: flowMeans Version: 1.64.0 Depends: R (>= 2.10.0) Imports: Biobase, graphics, grDevices, methods, rrcov, stats, feature, flowCore License: Artistic-2.0 Package: flowMerge Version: 2.52.0 Depends: graph,feature,flowClust,Rgraphviz,foreach,snow Imports: rrcov,flowCore, graphics, methods, stats, utils Suggests: knitr, rmarkdown Enhances: doMC, multicore License: Artistic-2.0 Package: flowPeaks Version: 1.50.0 Depends: R (>= 2.12.0) Suggests: flowCore License: Artistic-1.0 Archs: x64 Package: flowPloidy Version: 1.30.0 Imports: flowCore, car, caTools, knitr, rmarkdown, minpack.lm, shiny, methods, graphics, stats, utils Suggests: flowPloidyData, testthat License: GPL-3 Package: flowPlots Version: 1.52.0 Depends: R (>= 2.13.0), methods Suggests: vcd License: Artistic-2.0 Package: FlowSOM Version: 2.12.0 Depends: R (>= 4.0), igraph Imports: stats, utils, colorRamps, ConsensusClusterPlus, dplyr, flowCore, ggforce, ggnewscale, ggplot2, ggpubr, grDevices, magrittr, methods, rlang, Rtsne, tidyr, BiocGenerics, XML Suggests: BiocStyle, testthat, CytoML, flowWorkspace, ggrepel, scattermore, pheatmap, ggpointdensity License: GPL (>= 2) Archs: x64 Package: flowSpecs Version: 1.18.0 Depends: R (>= 4.0) Imports: ggplot2 (>= 3.1.0), BiocGenerics (>= 0.30.0), BiocParallel (>= 1.18.1), Biobase (>= 2.48.0), reshape2 (>= 1.4.3), flowCore (>= 1.50.0), zoo (>= 1.8.6), stats (>= 3.6.0), methods (>= 3.6.0) Suggests: testthat, knitr, rmarkdown, BiocStyle, DepecheR License: MIT + file LICENSE Package: flowStats Version: 4.16.0 Depends: R (>= 3.0.2) Imports: BiocGenerics, MASS, flowCore (>= 1.99.6), flowWorkspace, ncdfFlow(>= 2.19.5), flowViz, fda (>= 2.2.6), Biobase, methods, grDevices, graphics, stats, cluster, utils, KernSmooth, lattice, ks, RColorBrewer, rrcov, corpcor, mnormt, clue Suggests: xtable, testthat, openCyto, ggcyto, ggridges Enhances: RBGL,graph License: Artistic-2.0 Package: flowTime Version: 1.28.0 Depends: R (>= 3.4), flowCore Imports: utils, dplyr (>= 1.0.0), tibble, magrittr, plyr, rlang Suggests: knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, stats, flowClust, openCyto, flowStats, ggcyto License: Artistic-2.0 Package: flowTrans Version: 1.56.0 Depends: R (>= 2.11.0), flowCore, flowViz,flowClust Imports: flowCore, methods, flowViz, stats, flowClust License: Artistic-2.0 Package: flowViz Version: 1.68.0 Depends: R (>= 2.7.0), flowCore(>= 1.41.9), lattice Imports: stats4, Biobase, flowCore, graphics, grDevices, grid, KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer, stats, utils, hexbin,IDPmisc Suggests: colorspace, flowStats, knitr, rmarkdown, markdown, testthat License: Artistic-2.0 Package: flowVS Version: 1.36.0 Depends: R (>= 3.2), methods, flowCore, flowViz, flowStats Suggests: knitr, vsn, License: Artistic-2.0 Package: flowWorkspace Version: 4.16.0 Depends: R (>= 3.5.0) Imports: Biobase, BiocGenerics, cytolib (>= 2.13.1), XML, ggplot2, graph, graphics, grDevices, methods, stats, stats4, utils, RBGL, tools, Rgraphviz, data.table, dplyr, scales(>= 1.3.0), matrixStats, RProtoBufLib, flowCore(>= 2.1.1), ncdfFlow(>= 2.25.4), DelayedArray, S4Vectors LinkingTo: cpp11, BH(>= 1.62.0-1), RProtoBufLib(>= 1.99.4), cytolib (>= 2.3.7),Rhdf5lib Suggests: testthat, flowWorkspaceData (>= 2.23.2), knitr, rmarkdown, ggcyto, parallel, CytoML, openCyto License_restricts_use: no Archs: x64 Package: fmcsR Version: 1.46.0 Depends: R (>= 2.10.0), ChemmineR, methods Imports: RUnit, methods, ChemmineR, BiocGenerics, parallel Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap,rmarkdown License: Artistic-2.0 Archs: x64 Package: fmrs Version: 1.14.0 Depends: R (>= 4.3.0) Imports: methods, survival, stats Suggests: BiocGenerics, testthat, knitr, utils License: GPL-3 Archs: x64 Package: fobitools Version: 1.12.0 Depends: R (>= 4.1) Imports: clisymbols, crayon, dplyr, fgsea, ggplot2, ggraph, magrittr, ontologyIndex, purrr, RecordLinkage, stringr, textclean, tictoc, tidygraph, tidyr, vroom Suggests: BiocStyle, covr, ggrepel, kableExtra, knitr, metabolomicsWorkbenchR, POMA, rmarkdown, rvest, SummarizedExperiment, testthat (>= 2.3.2), tidyverse License: GPL-3 Package: FoldGO Version: 1.22.0 Depends: R (>= 4.0) Imports: topGO (>= 2.30.1), ggplot2 (>= 2.2.1), tidyr (>= 0.8.0), stats, methods Suggests: knitr, rmarkdown, devtools, kableExtra License: GPL-3 Package: FRASER Version: 2.0.0 Depends: BiocParallel, data.table, Rsamtools, SummarizedExperiment Imports: AnnotationDbi, BBmisc, Biobase, BiocGenerics, biomaRt, BSgenome, cowplot, DelayedArray (>= 0.5.11), DelayedMatrixStats, extraDistr, generics, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges, grDevices, ggplot2, ggrepel, HDF5Array, matrixStats, methods, OUTRIDER, pcaMethods, pheatmap, plotly, PRROC, RColorBrewer, rhdf5, Rsubread, R.utils, S4Vectors, stats, tibble, tools, utils, VGAM LinkingTo: RcppArmadillo, Rcpp Suggests: magick, BiocStyle, knitr, rmarkdown, testthat, covr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, rtracklayer, SGSeq, ggbio, biovizBase License: MIT + file LICENSE Archs: x64 Package: frenchFISH Version: 1.16.0 Imports: utils, MCMCpack, NHPoisson Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 Package: FRGEpistasis Version: 1.40.0 Depends: R (>= 2.15), MASS, fda, methods, stats Imports: utils License: GPL-2 Package: frma Version: 1.56.0 Depends: R (>= 2.10.0), Biobase (>= 2.6.0) Imports: Biobase, MASS, DBI, affy, methods, oligo, oligoClasses, preprocessCore, utils, BiocGenerics Suggests: hgu133afrmavecs, frmaExampleData License: GPL (>= 2) Package: frmaTools Version: 1.56.0 Depends: R (>= 2.10.0), affy Imports: Biobase, DBI, methods, preprocessCore, stats, utils Suggests: oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM, hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf, hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData License: GPL (>= 2) Package: FScanR Version: 1.14.0 Depends: R (>= 4.0) Imports: stats Suggests: knitr, rmarkdown License: Artistic-2.0 Package: FunChIP Version: 1.30.0 Depends: R (>= 3.5.0), GenomicRanges Imports: shiny, fda, doParallel, GenomicAlignments, Rcpp, methods, foreach, parallel, GenomeInfoDb, Rsamtools, grDevices, graphics, stats, RColorBrewer LinkingTo: Rcpp License: Artistic-2.0 Archs: x64 Package: funtooNorm Version: 1.28.0 Depends: R(>= 3.4) Imports: pls, matrixStats, minfi, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb, grDevices, graphics, stats Suggests: prettydoc, minfiData, knitr, rmarkdown License: GPL-3 Package: FuseSOM Version: 1.6.0 Depends: R (>= 4.2.0) Imports: psych, FCPS, analogue, coop, pheatmap, ggplotify, fastcluster, fpc, ggplot2, stringr, ggpubr, proxy, cluster, diptest, methods, SummarizedExperiment, stats, S4Vectors LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown, SingleCellExperiment License: GPL-2 Archs: x64 Package: GA4GHclient Version: 1.28.0 Depends: R (>= 3.5.0), S4Vectors Imports: BiocGenerics, Biostrings, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, jsonlite, methods, VariantAnnotation Suggests: AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) Package: GA4GHshiny Version: 1.26.0 Depends: GA4GHclient Imports: AnnotationDbi, BiocGenerics, dplyr, DT, GenomeInfoDb, openxlsx, GenomicFeatures, methods, purrr, S4Vectors, shiny, shinyjs, tidyr, shinythemes Suggests: BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 Package: gaga Version: 2.50.0 Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv Enhances: parallel License: GPL (>= 2) Archs: x64 Package: gage Version: 2.54.0 Depends: R (>= 3.5.0) Imports: graph, KEGGREST, AnnotationDbi, GO.db Suggests: pathview, gageData, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq2, edgeR, limma License: GPL (>= 2.0) Package: GAprediction Version: 1.30.0 Depends: R (>= 3.3) Imports: glmnet, stats, utils, Matrix Suggests: knitr, rmarkdown License: GPL (>= 2) Package: garfield Version: 1.32.0 Suggests: knitr License: GPL-3 Archs: x64 Package: GARS Version: 1.24.0 Depends: R (>= 3.5), ggplot2, cluster Imports: DaMiRseq, MLSeq, stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) Package: GateFinder Version: 1.24.0 Imports: splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP Suggests: RUnit, BiocGenerics License: Artistic-2.0 Package: gatom Version: 1.2.0 Depends: R (>= 4.3.0) Imports: data.table, igraph, BioNet, plyr, methods, XML, sna, intergraph, network, GGally, grid, ggplot2, mwcsr, pryr, htmlwidgets, htmltools, shinyCyJS (>= 1.0.0) Suggests: testthat, knitr, rmarkdown, KEGGREST, AnnotationDbi, org.Mm.eg.db, reactome.db, fgsea, readr, BiocStyle, R.utils License: MIT + file LICENCE Package: GBScleanR Version: 1.8.0 Depends: SeqArray Imports: stats, utils, methods, ggplot2, tidyr, expm, Rcpp, RcppParallel, gdsfmt LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown License: GPL-3 + file LICENSE Archs: x64 Package: gcapc Version: 1.28.0 Depends: R (>= 3.4) Imports: BiocGenerics, GenomeInfoDb, S4Vectors, IRanges, Biostrings, BSgenome, GenomicRanges, Rsamtools, GenomicAlignments, matrixStats, MASS, splines, grDevices, graphics, stats, methods Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: GPL-3 Package: gcatest Version: 2.4.0 Depends: R (>= 4.0) Imports: methods, lfa Suggests: knitr, ggplot2, testthat, BEDMatrix, genio License: GPL (>= 3) Package: gCrisprTools Version: 2.10.0 Depends: R (>= 4.1) Imports: Biobase, limma, RobustRankAggreg, ggplot2, SummarizedExperiment, grid, rmarkdown, grDevices, graphics, methods, ComplexHeatmap, stats, utils, parallel Suggests: edgeR, knitr, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea License: Artistic-2.0 Package: gcrma Version: 2.76.0 Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils Imports: Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector, Biostrings (>= 2.11.32), splines, BiocManager Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe License: LGPL Archs: x64 Package: GDCRNATools Version: 1.24.0 Depends: R (>= 3.5.0) Imports: shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2, clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival, survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons, BiocParallel Suggests: knitr, testthat, prettydoc, rmarkdown License: Artistic-2.0 Package: gDNAx Version: 1.2.0 Depends: R (>= 4.3) Imports: methods, BiocGenerics, BiocParallel, matrixStats, Biostrings, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, GenomicFiles, GenomicAlignments, GenomicFeatures, Rsamtools, AnnotationHub, RColorBrewer, AnnotationDbi, bitops, plotrix, SummarizedExperiment, grDevices, graphics, stats, utils, cli Suggests: BiocStyle, knitr, rmarkdown, RUnit, TxDb.Hsapiens.UCSC.hg38.knownGene, gDNAinRNAseqData License: Artistic-2.0 Package: gDR Version: 1.2.0 Depends: R (>= 4.2), gDRcore (>= 1.1.11), gDRimport (>= 1.1.4), gDRutils (>= 1.1.5) Suggests: BiocStyle, BumpyMatrix, futile.logger, gDRstyle (>= 1.1.3), gDRtestData (>= 1.1.7), kableExtra, knitr, markdown, purrr, rmarkdown, SummarizedExperiment, testthat, yaml License: Artistic-2.0 Package: gDRcore Version: 1.2.0 Depends: R (>= 4.2) Imports: BumpyMatrix, BiocParallel, checkmate, futile.logger, gDRutils (>= 1.1.3), MultiAssayExperiment, purrr, stringr, S4Vectors, SummarizedExperiment, data.table Suggests: BiocStyle, gDRstyle (>= 1.1.2), gDRimport (>= 1.1.4), gDRtestData (>= 1.1.6), IRanges, knitr, pkgbuild, qs, testthat, yaml License: Artistic-2.0 Archs: x64 Package: gDRimport Version: 1.2.0 Depends: R (>= 4.2) Imports: assertthat, BumpyMatrix, checkmate, CoreGx, PharmacoGx, data.table, futile.logger, gDRutils (>= 1.1.5), magrittr, methods, MultiAssayExperiment, readxl, rio, S4Vectors, stats, stringi, SummarizedExperiment, tibble, tools, utils, XML, yaml, openxlsx Suggests: BiocStyle, gDRtestData (>= 1.1.7), gDRstyle (>= 1.1.3), knitr, purrr, qs, testthat License: Artistic-2.0 Package: gDRstyle Version: 1.2.0 Depends: R (>= 4.2) Imports: BiocCheck, BiocManager, checkmate, desc, git2r, lintr (>= 3.0.0), rcmdcheck, remotes, yaml, rjson, pkgbuild, withr Suggests: BiocStyle, knitr, testthat (>= 3.0.0) License: Artistic-2.0 Package: gDRutils Version: 1.2.0 Depends: R (>= 4.2) Imports: BiocParallel, BumpyMatrix, checkmate, data.table, drc, jsonlite, jsonvalidate, methods, MultiAssayExperiment, S4Vectors, stats, stringr, SummarizedExperiment Suggests: BiocManager, BiocStyle, futile.logger, gDRstyle (>= 1.1.5), gDRtestData (>= 1.1.10), IRanges, knitr, lintr, purrr, qs, rcmdcheck, rmarkdown, testthat, tools, yaml License: Artistic-2.0 Package: GDSArray Version: 1.24.2 Depends: R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray (>= 0.5.32) Imports: tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, BiocManager License: GPL-3 Package: gdsfmt Version: 1.40.0 Depends: R (>= 2.15.0), methods Suggests: parallel, digest, Matrix, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics License: LGPL-3 Archs: x64 Package: GeDi Version: 1.0.1 Depends: R (>= 4.4.0) Imports: GOSemSim, Matrix, shiny, shinyWidgets, bs4Dash, rintrojs, utils, DT, dplyr, shinyBS, STRINGdb, igraph, visNetwork, shinycssloaders, fontawesome, grDevices, parallel, stats, ggplot2, plotly, GeneTonic, RColorBrewer, scales, readxl, ggdendro, ComplexHeatmap, BiocNeighbors, tm, wordcloud2, tools, BiocParallel, BiocFileCache Suggests: knitr, rmarkdown, testthat (>= 3.0.0), DESeq2, htmltools, pcaExplorer, AnnotationDbi, macrophage, topGO, biomaRt, ReactomePA, clusterProfiler, BiocStyle, org.Hs.eg.db License: MIT + file LICENSE Package: GEM Version: 1.30.0 Depends: R (>= 3.3) Imports: tcltk, ggplot2, methods, stats, grDevices, graphics, utils Suggests: knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown License: Artistic-2.0 Package: gemini Version: 1.18.0 Depends: R (>= 4.1.0) Imports: dplyr, grDevices, ggplot2, magrittr, mixtools, scales, pbmcapply, parallel, stats, utils Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE Package: gemma.R Version: 3.0.8 Imports: magrittr, glue, memoise, jsonlite, data.table, rlang, lubridate, utils, stringr, SummarizedExperiment, Biobase, tibble, tidyr, S4Vectors, httr, rappdirs, bit64, assertthat, digest, R.utils, base64enc Suggests: testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis, poolr, kableExtra, listviewer, shiny License: Apache License (>= 2) Package: genArise Version: 1.80.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes Package: geneAttribution Version: 1.30.0 Imports: utils, GenomicRanges, org.Hs.eg.db, BiocGenerics, GenomeInfoDb, GenomicFeatures, IRanges, rtracklayer Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat License: Artistic-2.0 Package: GeneBreak Version: 1.34.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 Package: geneClassifiers Version: 1.28.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 Package: GeneExpressionSignature Version: 1.50.0 Depends: R (>= 4.0) Imports: Biobase, stats, methods Suggests: apcluster, GEOquery, knitr, rmarkdown, BiocStyle License: GPL-2 Package: genefilter Version: 1.86.0 Imports: MatrixGenerics (>= 1.11.1), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival, grDevices Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr License: Artistic-2.0 Archs: x64 Package: genefu Version: 2.36.0 Depends: R (>= 4.1), survcomp, biomaRt, iC10, AIMS Imports: amap, impute, mclust, limma, graphics, stats, utils Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival, BiocStyle, magick, rmarkdown License: Artistic-2.0 Package: GeneGeneInteR Version: 1.30.0 Depends: R (>= 4.0) Imports: snpStats, mvtnorm, Rsamtools, igraph, kernlab, FactoMineR, IRanges, GenomicRanges, data.table,grDevices, graphics,stats, utils, methods License: GPL (>= 2) Archs: x64 Package: GeneMeta Version: 1.76.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 Package: GeneNetworkBuilder Version: 1.46.0 Depends: R (>= 2.15.1), Rcpp (>= 0.9.13) Imports: plyr, graph, htmlwidgets, Rgraphviz, rjson, XML, methods, grDevices, stats, graphics LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db License: GPL (>= 2) Archs: x64 Package: GeneOverlap Version: 1.40.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 Package: geneplast Version: 1.30.0 Depends: R (>= 4.0), methods Imports: igraph, snow, ape, grDevices, graphics, stats, utils, data.table Suggests: RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data, geneplast.data.string.v91, ggplot2, ggpubr, plyr License: GPL (>= 2) Package: geneplotter Version: 1.82.0 Depends: R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate Imports: AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats, utils Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db, BiocStyle, knitr License: Artistic-2.0 Package: geneRecommender Version: 1.76.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) Package: GeneRegionScan Version: 1.60.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) Package: geneRxCluster Version: 1.40.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) Archs: x64 Package: GeneSelectMMD Version: 2.48.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) Archs: x64 Package: GENESIS Version: 2.34.0 Imports: Biobase, BiocGenerics, BiocParallel, GWASTools, gdsfmt, GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate, data.table, graphics, grDevices, igraph, Matrix, methods, reshape2, stats, utils Suggests: CompQuadForm, COMPoissonReg, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 Archs: x64 Package: GeneStructureTools Version: 1.24.0 Imports: Biostrings,GenomicRanges,IRanges,data.table,plyr,stringdist,stringr,S4Vectors,BSgenome.Mmusculus.UCSC.mm10,stats,utils,Gviz,rtracklayer,methods Suggests: BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE Package: geNetClassifier Version: 1.44.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods Imports: e1071, graphics, grDevices Suggests: leukemiasEset, RUnit, BiocGenerics Enhances: RColorBrewer, igraph, infotheo License: GPL (>= 2) Package: GeneticsPed Version: 1.66.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE Archs: x64 Package: GeneTonic Version: 2.8.0 Depends: R (>= 4.0.0) Imports: AnnotationDbi, backbone, bs4Dash (>= 2.0.0), circlize, colorspace, colourpicker, ComplexHeatmap, ComplexUpset, dendextend, DESeq2, dplyr, DT, dynamicTreeCut, expm, ggforce, ggplot2 (>= 3.5.0), ggrepel, ggridges, GO.db, graphics, grDevices, grid, igraph, matrixStats, methods, plotly, RColorBrewer, rintrojs, rlang, rmarkdown, S4Vectors, scales, shiny, shinyAce, shinycssloaders, shinyWidgets, stats, SummarizedExperiment, tidyr, tippy, tools, utils, viridis, visNetwork Suggests: knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0) License: MIT + file LICENSE Package: geneXtendeR Version: 1.30.0 Depends: rtracklayer, GO.db, R (>= 3.5.0) Imports: data.table, dplyr, graphics, networkD3, RColorBrewer, SnowballC, tm, utils, wordcloud, AnnotationDbi, BiocStyle, org.Rn.eg.db Suggests: knitr, rmarkdown, testthat, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Pt.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer License: GPL (>= 3) Archs: x64 Package: GENIE3 Version: 1.26.0 Imports: stats, reshape2, dplyr Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods, BiocStyle License: GPL (>= 2) Archs: x64 Package: genoCN Version: 1.56.0 Imports: graphics, stats, utils License: GPL (>= 2) Archs: x64 Package: genomation Version: 1.36.0 Depends: R (>= 3.5.0), grid Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table, GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute, IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern, rtracklayer (>= 1.39.7), Rcpp (>= 0.12.14) LinkingTo: Rcpp Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown, RUnit License: Artistic-2.0 Archs: x64 Package: GenomAutomorphism Version: 1.6.0 Depends: R (>= 4.4.0), Imports: Biostrings, BiocGenerics, BiocParallel, GenomeInfoDb, GenomicRanges, IRanges, matrixStats, XVector, dplyr, data.table, parallel, doParallel, foreach, methods, S4Vectors, stats, numbers, utils Suggests: spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr License: Artistic-2.0 Package: GenomeInfoDb Version: 1.40.1 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.25.12), IRanges (>= 2.13.12) Imports: stats, stats4, utils, UCSC.utils, GenomeInfoDbData Suggests: R.utils, data.table, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr License: Artistic-2.0 Package: genomeIntervals Version: 1.60.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: GenomeInfoDb (>= 1.5.8), GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 Package: genomes Version: 3.34.0 Depends: readr, curl License: GPL-3 Package: GenomicAlignments Version: 1.40.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.55.3), SummarizedExperiment (>= 1.9.13), Biostrings (>= 2.55.7), Rsamtools (>= 1.31.2) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel LinkingTo: S4Vectors, IRanges Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, knitr, BiocStyle License: Artistic-2.0 Archs: x64 Package: GenomicDataCommons Version: 1.28.0 Depends: R (>= 3.4.0), magrittr Imports: stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, tibble, tidyr Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools, BiocParallel, TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation, maftools, R.utils, data.table License: Artistic-2.0 Package: GenomicDistributions Version: 1.12.0 Depends: R (>= 4.0), IRanges, GenomicRanges Imports: data.table, ggplot2, reshape2, methods, utils, Biostrings, plyr, dplyr, scales, broom, GenomeInfoDb, stats Suggests: AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle, rmarkdown, GenomicDistributionsData Enhances: BSgenome, extrafont, ensembldb, GenomicFeatures License: BSD_2_clause + file LICENSE Package: GenomicFeatures Version: 1.56.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.29), IRanges (>= 2.37.1), GenomeInfoDb (>= 1.35.8), GenomicRanges (>= 1.55.2), AnnotationDbi (>= 1.41.4) Imports: methods, utils, stats, DBI, XVector, Biostrings, rtracklayer Suggests: txdbmaker, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, AnnotationFilter, RUnit, BiocStyle, knitr, markdown License: Artistic-2.0 Package: GenomicFiles Version: 1.40.0 Depends: R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), MatrixGenerics, GenomicRanges (>= 1.31.16), SummarizedExperiment, BiocParallel (>= 1.1.0), Rsamtools (>= 1.17.29), rtracklayer (>= 1.25.3) Imports: GenomicAlignments (>= 1.7.7), IRanges, S4Vectors (>= 0.9.25), VariantAnnotation (>= 1.27.9), GenomeInfoDb Suggests: BiocStyle, RUnit, genefilter, deepSNV, snpStats, knitr, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens License: Artistic-2.0 Package: genomicInstability Version: 1.10.0 Depends: R (>= 4.1.0), checkmate Imports: mixtools, SummarizedExperiment Suggests: SingleCellExperiment, ExperimentHub, pROC License: file LICENSE Package: GenomicInteractionNodes Version: 1.8.0 Depends: R (>= 4.2.0), stats Imports: AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures, GenomeInfoDb, methods, IRanges, RBGL, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: file LICENSE Package: GenomicInteractions Version: 1.38.0 Depends: R (>= 3.5), InteractionSet Imports: Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges, BiocGenerics (>= 0.15.3), data.table, stringr, GenomeInfoDb, ggplot2, grid, gridExtra, methods, igraph, S4Vectors (>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils, grDevices Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 Package: GenomicOZone Version: 1.18.0 Depends: R (>= 4.0.0), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges, biomaRt, ggplot2 Imports: grDevices, stats, utils, plyr, gridExtra, lsr, parallel, ggbio, S4Vectors, IRanges, GenomeInfoDb, Rdpack Suggests: readxl, GEOquery, knitr, rmarkdown License: LGPL (>= 3) Package: GenomicPlot Version: 1.2.3 Depends: R (>= 4.4.0), GenomicRanges (>= 1.46.1) Imports: methods, Rsamtools, parallel, tidyr, rtracklayer (>= 1.54.0), plyranges (>= 1.14.0), cowplot (>= 1.1.1), VennDiagram, ggplotify, GenomeInfoDb, IRanges, ComplexHeatmap, RCAS (>= 1.20.0), scales (>= 1.2.0), GenomicAlignments (>= 1.30.0), edgeR, circlize, viridis, ggsignif (>= 0.6.3), ggsci (>= 2.9), ggpubr, grDevices, graphics, stats, utils, GenomicFeatures, genomation (>= 1.36.0), txdbmaker, ggplot2 (>= 3.3.5), BiocGenerics, dplyr, grid Suggests: knitr, rmarkdown, R.utils, Biobase, BiocStyle, testthat, AnnotationDbi License: GPL-2 Package: GenomicRanges Version: 1.56.1 Depends: R (>= 4.0.0), methods, stats4, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.37.1), GenomeInfoDb (>= 1.15.2) Imports: utils, stats, XVector (>= 0.29.2) LinkingTo: S4Vectors, IRanges Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, txdbmaker, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle License: Artistic-2.0 Archs: x64 Package: GenomicScores Version: 2.16.0 Depends: R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods, BiocGenerics (>= 0.13.8) Imports: stats, utils, XML, httr, Biobase, BiocManager, BiocFileCache, IRanges (>= 2.3.23), Biostrings, GenomeInfoDb, AnnotationHub, rhdf5, DelayedArray, HDF5Array Suggests: RUnit, BiocStyle, knitr, rmarkdown, VariantAnnotation, gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader, data.table, DT, magrittr, shinydashboard, BSgenome.Hsapiens.UCSC.hg38, phastCons100way.UCSC.hg38, MafDb.1Kgenomes.phase1.hs37d5, MafH5.gnomAD.v4.0.GRCh38, SNPlocs.Hsapiens.dbSNP144.GRCh37, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 Package: GenomicSuperSignature Version: 1.12.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable, irlba Suggests: knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis, BiocStyle, testthat, forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils License: Artistic-2.0 Package: GenomicTuples Version: 1.38.0 Depends: R (>= 4.0), GenomicRanges (>= 1.37.4), GenomeInfoDb (>= 1.15.2), S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.19.13), data.table, stats4, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, covr, GenomicAlignments, Biostrings License: Artistic-2.0 Archs: x64 Package: GenProSeq Version: 1.8.0 Depends: keras, mclust, R (>= 4.2) Imports: tensorflow, word2vec, DeepPINCS, ttgsea, CatEncoders, reticulate, stats Suggests: VAExprs, stringdist, knitr, testthat, rmarkdown License: Artistic-2.0 Package: GenVisR Version: 1.36.0 Depends: R (>= 3.3.0), methods Imports: AnnotationDbi, biomaRt (>= 2.45.8), BiocGenerics, Biostrings, DBI, GenomicFeatures, GenomicRanges (>= 1.25.4), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0), gtable, gtools, IRanges (>= 2.7.5), plyr (>= 1.8.3), reshape2, Rsamtools, scales, viridis, data.table, BSgenome, GenomeInfoDb, VariantAnnotation Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38 License: GPL-3 + file LICENSE Package: GeoDiff Version: 1.10.0 Depends: R (>= 4.1.0), Biobase Imports: Matrix, robust, plyr, lme4, Rcpp (>= 1.0.4.6), withr, methods, graphics, stats, testthat, GeomxTools, NanoStringNCTools LinkingTo: Rcpp, RcppArmadillo, roptim Suggests: knitr, rmarkdown, dplyr License: MIT + file LICENSE Archs: x64 Package: GEOexplorer Version: 1.10.0 Depends: shiny, limma, Biobase, plotly, enrichR, R (>= 4.1.0) Imports: DT, XML, httr, sva, xfun, edgeR, htmltools, factoextra, heatmaply, pheatmap, scales, shinyHeatmaply, shinybusy, ggplot2, stringr, umap, GEOquery, impute, grDevices, stats, graphics, markdown, knitr, utils, xml2, R.utils, readxl, shinycssloaders, car Suggests: rmarkdown, usethis, testthat (>= 3.0.0) License: GPL-3 Package: GEOfastq Version: 1.12.0 Imports: xml2, rvest, stringr, RCurl, doParallel, foreach, plyr Suggests: BiocCheck, roxygen2, knitr, rmarkdown, testthat License: MIT + file LICENSE Package: GEOmetadb Version: 1.66.0 Depends: GEOquery,RSQLite Suggests: knitr, rmarkdown, dplyr, dbplyr, tm, wordcloud License: Artistic-2.0 Package: GeomxTools Version: 3.8.0 Depends: R (>= 3.6), Biobase, NanoStringNCTools, S4Vectors Imports: BiocGenerics, rjson, readxl, EnvStats, reshape2, methods, utils, stats, data.table, lmerTest, dplyr, stringr, grDevices, graphics, GGally, rlang, ggplot2, SeuratObject Suggests: rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork License: MIT Package: GEOquery Version: 2.72.0 Depends: methods, Biobase Imports: readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr, limma, curl, R.utils Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr, markdown License: MIT Package: GEOsubmission Version: 1.56.0 Imports: affy, Biobase, utils License: GPL (>= 2) Package: GeoTcgaData Version: 2.4.0 Depends: R (>= 4.2.0) Imports: utils, data.table, plyr, cqn, topconfects, stats, SummarizedExperiment, methods Suggests: knitr, rmarkdown, DESeq2, S4Vectors, ChAMP, impute, tidyr, clusterProfiler, org.Hs.eg.db, edgeR, limma, quantreg, minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, dearseq, NOISeq, testthat (>= 3.0.0), CATT, TCGAbiolinks, enrichplot, GEOquery, BiocGenerics License: Artistic-2.0 Package: gep2pep Version: 1.24.0 Imports: repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods, Biobase, XML, rhdf5, digest, iterators Suggests: WriteXLS, testthat, knitr, rmarkdown License: GPL-3 Package: gespeR Version: 1.36.0 Depends: methods, graphics, ggplot2, R(>= 2.10) Imports: Matrix, glmnet, cellHTS2, Biobase, biomaRt, doParallel, parallel, foreach, reshape2, dplyr Suggests: knitr License: GPL-3 Package: getDEE2 Version: 1.14.0 Depends: R (>= 4.0) Imports: stats, utils, SummarizedExperiment, htm2txt Suggests: knitr, testthat, rmarkdown License: GPL-3 Package: geva Version: 1.12.0 Depends: R (>= 4.1) Imports: grDevices, graphics, methods, stats, utils, dbscan, fastcluster, matrixStats Suggests: devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat (>= 3.0.0) License: LGPL-3 Package: GEWIST Version: 1.48.0 Depends: R (>= 2.10), car License: GPL-2 Package: gg4way Version: 1.2.0 Depends: R (>= 4.3.0), ggplot2 Imports: DESeq2, dplyr, edgeR, ggrepel, glue, janitor, limma, magrittr, methods, purrr, rlang, scales, stats, stringr, tibble, tidyr Suggests: airway, BiocStyle, knitr, org.Hs.eg.db, rmarkdown, testthat License: MIT + file LICENSE Package: ggbio Version: 1.52.0 Depends: methods, BiocGenerics, ggplot2 (>= 1.0.0) Imports: grid, grDevices, graphics, stats, utils, gridExtra, scales, reshape2, gtable, Hmisc, biovizBase (>= 1.29.2), Biobase, S4Vectors (>= 0.13.13), IRanges (>= 2.11.16), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.29.14), SummarizedExperiment, Biostrings, Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), BSgenome, VariantAnnotation (>= 1.11.4), rtracklayer (>= 1.25.16), GenomicFeatures (>= 1.29.11), OrganismDbi, GGally, ensembldb (>= 1.99.13), AnnotationDbi, AnnotationFilter, rlang Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex License: Artistic-2.0 Package: ggcyto Version: 1.32.0 Depends: methods, ggplot2(>= 3.5.0), flowCore(>= 1.41.5), ncdfFlow(>= 2.17.1), flowWorkspace(>= 4.3.1) Imports: plyr, scales, hexbin, data.table, RColorBrewer, gridExtra, rlang Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr License: file LICENSE Package: ggkegg Version: 1.2.2 Depends: R (>= 4.3.0), ggplot2, ggraph, XML, igraph, tidygraph Imports: BiocFileCache, GetoptLong, data.table, dplyr, magick, patchwork, shadowtext, stringr, tibble, org.Hs.eg.db, methods, utils, stats, AnnotationDbi, grDevices, gtable Suggests: knitr, clusterProfiler, bnlearn, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE Package: ggmanh Version: 1.8.0 Depends: methods, ggplot2 Imports: gdsfmt, ggrepel, grDevices, RColorBrewer, rlang, scales, SeqArray (>= 1.32.0), stats Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0), markdown, GenomicRanges License: MIT + file LICENSE Package: ggmsa Version: 1.10.0 Depends: R (>= 4.1.0) Imports: Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot, RColorBrewer, ggalt, ggforce, dplyr, R4RNA, grDevices, seqmagick, grid, methods, statebins, ggtree (>= 1.17.1) Suggests: ggtreeExtra, ape, cowplot, knitr, BiocStyle, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0) License: Artistic-2.0 Package: GGPA Version: 1.16.0 Depends: R (>= 4.0.0), stats, methods, graphics, GGally, network, sna, scales, matrixStats Imports: Rcpp (>= 0.11.3) LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle License: GPL (>= 2) Archs: x64 Package: ggsc Version: 1.2.0 Imports: Rcpp, RcppParallel, cli, dplyr, ggfun, ggplot2, grDevices, grid, methods, rlang, scattermore, stats, Seurat, SingleCellExperiment, SummarizedExperiment, tidydr, tidyr, tibble, utils, RColorBrewer, yulab.utils, scales LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: aplot, BiocParallel, forcats, ggforce, ggnewscale, igraph, knitr, ks, Matrix, prettydoc, rmarkdown, scran, scater, scatterpie, scuttle, shadowtext, sf, SeuratObject, SpatialExperiment, STexampleData, testthat (>= 3.0.0) License: Artistic-2.0 Archs: x64 Package: ggspavis Version: 1.10.0 Depends: ggplot2 Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, ggside, grid, ggrepel, RColorBrewer, scales, grDevices, methods, stats Suggests: BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix, scater, scran, uwot, testthat, patchwork License: MIT + file LICENSE Package: ggtree Version: 3.12.0 Depends: R (>= 3.5.0) Imports: ape, aplot, dplyr, ggplot2 (> 3.3.6), grid, magrittr, methods, purrr, rlang, ggfun (>= 0.0.9), yulab.utils, tidyr, tidytree (>= 0.4.5), treeio (>= 1.8.0), utils, scales, stats, cli Suggests: emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, testthat, tibble, glue License: Artistic-2.0 Package: ggtreeDendro Version: 1.6.0 Depends: ggtree (>= 3.5.3) Imports: ggplot2, stats, tidytree, utils Suggests: aplot, cluster, knitr, MASS, mdendro, prettydoc, pvclust, rmarkdown, testthat (>= 3.0.0), treeio, yulab.utils License: Artistic-2.0 Package: ggtreeExtra Version: 1.14.0 Imports: ggplot2, utils, rlang, ggnewscale, stats, ggtree, tidytree (>= 0.3.9), cli, magrittr Suggests: treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc, markdown, testthat (>= 3.0.0), pillar License: GPL (>= 3) Package: ggtreeSpace Version: 1.0.0 Imports: interp, ape, dplyr, GGally, ggplot2, grid, ggtree, phytools, rlang, tibble, tidyr, tidyselect, stats Suggests: knitr, prettydoc, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 Package: GIGSEA Version: 1.22.0 Depends: R (>= 3.5), Matrix, MASS, locfdr, stats, utils Suggests: knitr, rmarkdown License: LGPL-3 Package: ginmappeR Version: 1.0.2 Imports: KEGGREST, UniProt.ws, XML, rentrez, httr, utils, memoise, cachem Suggests: RUnit, BiocGenerics, markdown, knitr License: GPL-3 + file LICENSE Package: gINTomics Version: 1.0.0 Depends: R (>= 4.4.0) Imports: BiocParallel, biomaRt, OmnipathR, edgeR, ggplot2, ggridges, gtools, MultiAssayExperiment, plyr, stringi, stringr, SummarizedExperiment, methods, stats, reshape2, randomForest, limma, org.Hs.eg.db, org.Mm.eg.db, BiocGenerics, GenomicFeatures, ReactomePA, clusterProfiler, dplyr, AnnotationDbi, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, shiny, GenomicRanges, ggtree, shinydashboard, plotly, DT, MASS, InteractiveComplexHeatmap, ComplexHeatmap, visNetwork, shiny.gosling, ggvenn, RColorBrewer, utils, grDevices, callr, circlize Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 Package: girafe Version: 1.56.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.25), Rsamtools (>= 1.31.2), intervals (>= 0.13.1), ShortRead (>= 1.37.1), genomeIntervals (>= 1.25.1), grid Imports: methods, Biobase, Biostrings (>= 2.47.6), pwalign, graphics, grDevices, stats, utils, IRanges (>= 2.13.12) Suggests: MASS, org.Mm.eg.db, RColorBrewer Enhances: genomeIntervals License: Artistic-2.0 Archs: x64 Package: GLAD Version: 2.68.0 Depends: R (>= 2.10) Imports: aws License: GPL-2 Archs: x64 Package: GladiaTOX Version: 1.20.0 Depends: R (>= 3.6.0), data.table (>= 1.9.4) Imports: DBI, RMariaDB, RSQLite, numDeriv, RColorBrewer, parallel, stats, methods, graphics, grDevices, xtable, tools, brew, stringr, RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML Suggests: roxygen2, knitr, rmarkdown, testthat, BiocStyle License: GPL-2 Package: Glimma Version: 2.14.0 Depends: R (>= 4.0.0) Imports: htmlwidgets, edgeR, DESeq2, limma, SummarizedExperiment, stats, jsonlite, methods, S4Vectors Suggests: testthat, knitr, rmarkdown, BiocStyle, IRanges, GenomicRanges, pryr, AnnotationHub, scRNAseq, scater, scran License: GPL-3 Package: glmGamPoi Version: 1.16.0 Imports: Rcpp, DelayedMatrixStats, matrixStats, MatrixGenerics, DelayedArray, HDF5Array, SummarizedExperiment, SingleCellExperiment, BiocGenerics, methods, stats, utils, splines, rlang, vctrs LinkingTo: Rcpp, RcppArmadillo, beachmat Suggests: testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, beachmat, MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown, BiocStyle, TENxPBMCData, muscData, scran, Matrix, dplyr License: GPL-3 Archs: x64 Package: glmSparseNet Version: 1.22.0 Depends: R (>= 4.3.0) Imports: biomaRt, checkmate, dplyr, forcats, futile.logger, ggplot2, glue, httr, lifecycle, methods, parallel, readr, rlang, glmnet, Matrix, MultiAssayExperiment, SummarizedExperiment, survminer, TCGAutils, utils Suggests: BiocStyle, curatedTCGAData, knitr, magrittr, reshape2, pROC, rmarkdown, survival, testthat, VennDiagram, withr License: GPL-3 Package: GlobalAncova Version: 4.22.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM Suggests: GO.db, golubEsets, hu6800.db, vsn, Rgraphviz License: GPL (>= 2) Archs: x64 Package: globalSeq Version: 1.32.0 Depends: R (>= 3.0.0) Suggests: knitr, testthat, SummarizedExperiment, S4Vectors License: GPL-3 Package: globaltest Version: 5.58.0 Depends: methods, survival Imports: Biobase, AnnotationDbi, annotate, graphics Suggests: vsn, golubEsets, KEGGREST, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS, boot, rpart, mstate License: GPL (>= 2) Package: GloScope Version: 1.2.0 Depends: R (>= 4.3.0) Imports: utils, stats, MASS, mclust, ggplot2, RANN, FNN, BiocParallel, mvnfast, SingleCellExperiment, rlang Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown, zellkonverter License: Artistic-2.0 Package: GmicR Version: 1.18.0 Imports: AnnotationDbi, ape, bnlearn, Category, DT, doParallel, foreach, gRbase, GSEABase, gRain, GOstats, org.Hs.eg.db, org.Mm.eg.db, shiny, WGCNA, data.table, grDevices, graphics, reshape2, stats, utils Suggests: knitr, rmarkdown, testthat License: GPL-2 + file LICENSE Package: gmoviz Version: 1.16.0 Depends: circlize, GenomicRanges, graphics, R (>= 4.0) Imports: grid, gridBase, Rsamtools, ComplexHeatmap, BiocGenerics, Biostrings, GenomeInfoDb, methods, GenomicAlignments, GenomicFeatures, IRanges, rtracklayer, pracma, colorspace, S4Vectors Suggests: testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle, BiocManager License: GPL-3 Package: GMRP Version: 1.32.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) Package: GNET2 Version: 1.20.0 Depends: R (>= 3.6) Imports: ggplot2,xgboost,Rcpp,reshape2,grid,DiagrammeR,methods,stats,matrixStats,graphics,SummarizedExperiment,dplyr,igraph, grDevices, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: Apache License 2.0 Archs: x64 Package: GNOSIS Version: 1.2.0 Depends: R (>= 4.3.0), shiny, shinydashboard, shinydashboardPlus, dashboardthemes, shinyWidgets, shinymeta, tidyverse, operator.tools, maftools Imports: DT, fontawesome, shinycssloaders, cBioPortalData, shinyjs, reshape2, RColorBrewer, survival, survminer, stats, compareGroups, rpart, partykit, DescTools, car, rstatix, fabricatr, shinylogs, magrittr Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE Package: GOexpress Version: 1.38.0 Depends: R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0) Imports: biomaRt (>= 2.18.0), stringr (>= 0.6.2), ggplot2 (>= 0.9.0), RColorBrewer (>= 1.0), gplots (>= 2.13.0), randomForest (>= 4.6), RCurl (>= 1.95) Suggests: BiocStyle License: GPL (>= 3) Package: GOfuncR Version: 1.24.0 Depends: R (>= 3.4), vioplot (>= 0.2), Imports: Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0), GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils, grDevices, graphics, stats, LinkingTo: Rcpp Suggests: Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat License: GPL (>= 2) Archs: x64 Package: GOpro Version: 1.30.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, dendextend, doParallel, foreach, parallel, org.Hs.eg.db, GO.db, Rcpp, stats, graphics, MultiAssayExperiment, IRanges, S4Vectors LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat License: GPL-3 Archs: x64 Package: goProfiles Version: 1.66.0 Depends: Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr Suggests: org.Hs.eg.db License: GPL-2 Package: GOSemSim Version: 2.30.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, GO.db, methods, rlang, stats, utils, yulab.utils LinkingTo: Rcpp Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, readr, rmarkdown, testthat, tidyr, tidyselect, ROCR License: Artistic-2.0 Archs: x64 Package: goseq Version: 1.56.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2) Imports: mgcv, graphics, stats, utils, AnnotationDbi, GO.db,BiocGenerics Suggests: edgeR, org.Hs.eg.db, rtracklayer License: LGPL (>= 2) Package: GOSim Version: 1.42.0 Depends: GO.db, annotate Imports: org.Hs.eg.db, AnnotationDbi, topGO, cluster, flexmix, RBGL, graph, Matrix, corpcor, Rcpp LinkingTo: Rcpp Enhances: igraph License: GPL (>= 2) Archs: x64 Package: goSorensen Version: 1.6.0 Depends: R (>= 4.3.0) Imports: GO.db, org.Hs.eg.db, goProfiles, stats, clusterProfiler, parallel, stringr Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 Package: goSTAG Version: 1.28.0 Depends: R (>= 3.4) Imports: AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 Package: GOstats Version: 2.70.0 Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.43.2), graph Imports: methods, stats, stats4, AnnotationDbi (>= 0.0.89), GO.db (>= 1.13.0), RBGL, annotate (>= 1.13.2), AnnotationForge, Rgraphviz Suggests: hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics, BiocStyle, knitr License: Artistic-2.0 Package: GOTHiC Version: 1.40.0 Depends: R (>= 3.5.0), methods, GenomicRanges, Biostrings, BSgenome, data.table Imports: BiocGenerics, S4Vectors (>= 0.9.38), IRanges, Rsamtools, ShortRead, rtracklayer, ggplot2, BiocManager, grDevices, utils, stats, GenomeInfoDb Suggests: HiCDataLymphoblast Enhances: parallel License: GPL-3 Package: goTools Version: 1.78.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 Package: GPA Version: 1.16.0 Depends: R (>= 4.0.0), methods, graphics, Rcpp Imports: parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS, stats, utils, grDevices LinkingTo: Rcpp Suggests: gpaExample License: GPL (>= 2) Archs: x64 Package: gpls Version: 1.76.0 Imports: stats Suggests: MASS License: Artistic-2.0 Package: gpuMagic Version: 1.20.0 Depends: R (>= 3.6.0), methods, utils Imports: Deriv, DescTools, digest, pryr, stringr, BiocGenerics LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 Archs: x64 Package: GrafGen Version: 1.0.0 Depends: R (>= 4.3.0) Imports: stats, utils, graphics, ggplot2, plotly, zlibbioc, scales, RColorBrewer, dplyr, grDevices, GenomicRanges, shiny, cowplot, ggpubr, stringr, rlang Suggests: knitr, rmarkdown, RUnit, BiocManager, BiocGenerics, BiocStyle, devtools License: GPL-2 Archs: x64 Package: GRaNIE Version: 1.8.0 Depends: R (>= 4.2.0) Imports: futile.logger, checkmate, patchwork, reshape2, data.table, matrixStats, Matrix, GenomicRanges, RColorBrewer, ComplexHeatmap, DESeq2, circlize, progress, utils, methods, stringr, tools, scales, igraph, S4Vectors, ggplot2, rlang, Biostrings, GenomeInfoDb (>= 1.34.8), SummarizedExperiment, forcats, gridExtra, limma, tidyselect, readr, grid, tidyr, dplyr, stats, grDevices, graphics, magrittr, tibble, viridis, colorspace, biomaRt, topGO, AnnotationHub, ensembldb Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Mmulatta.UCSC.rheMac10, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn6.refGene, TxDb.Rnorvegicus.UCSC.rn7.refGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Mmulatta.UCSC.rheMac10.refGene, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, org.Mmu.eg.db, IHW, clusterProfiler, ReactomePA, DOSE, BiocFileCache, ChIPseeker, testthat (>= 3.0.0), BiocStyle, csaw, BiocParallel, WGCNA, variancePartition, purrr, EDASeq, JASPAR2022, JASPAR2024, TFBSTools, motifmatchr, rbioapi, LDlinkR License: Artistic-2.0 Package: granulator Version: 1.12.0 Depends: R (>= 4.1) Imports: cowplot, e1071, epiR, dplyr, dtangle, ggplot2, ggplotify, grDevices, limSolve, magrittr, MASS, nnls, parallel, pheatmap, purrr, rlang, stats, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 Package: graper Version: 1.20.0 Depends: R (>= 3.6) Imports: Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats LinkingTo: Rcpp, RcppArmadillo, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) Archs: x64 Package: graph Version: 1.82.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.11) Imports: stats, stats4, utils Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle, knitr Enhances: Rgraphviz License: Artistic-2.0 Archs: x64 Package: GraphAlignment Version: 1.68.0 License: file LICENSE License_restricts_use: yes Archs: x64 Package: GraphAT Version: 1.76.0 Depends: R (>= 2.10), graph, methods Imports: graph, MCMCpack, methods, stats License: LGPL Package: graphite Version: 1.50.0 Depends: R (>= 4.2), methods Imports: AnnotationDbi, graph (>= 1.67.1), httr, rappdirs, stats, utils, graphics, rlang, purrr Suggests: checkmate, a4Preproc, ALL, BiocStyle, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) License: AGPL-3 Package: GraphPAC Version: 1.46.0 Depends: R(>= 2.15),iPAC, igraph, TSP, RMallow Suggests: RUnit, BiocGenerics License: GPL-2 Package: GRENITS Version: 1.56.0 Depends: R (>= 2.12.0), Rcpp (>= 0.8.6), RcppArmadillo (>= 0.2.8), ggplot2 (>= 0.9.0) Imports: graphics, grDevices, reshape2, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: network License: GPL (>= 2) Archs: x64 Package: GreyListChIP Version: 1.36.0 Depends: R (>= 4.0), methods, GenomicRanges Imports: GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, GenomeInfoDb, SummarizedExperiment, stats, utils Suggests: BiocStyle, BiocGenerics, RUnit, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 Package: GRmetrics Version: 1.30.0 Depends: R (>= 4.0), SummarizedExperiment Imports: drc, plotly, ggplot2, S4Vectors, stats Suggests: knitr, rmarkdown, BiocStyle, tinytex License: GPL-3 Package: groHMM Version: 1.38.0 Depends: R (>= 3.0.2), MASS, parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), rtracklayer (>= 1.39.7) Suggests: BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 Archs: x64 Package: GSALightning Version: 1.32.0 Depends: R (>= 3.3.0) Imports: Matrix, data.table, stats Suggests: knitr, rmarkdown License: GPL (>= 2) Package: GSAR Version: 1.38.0 Depends: R (>= 3.0.1), igraph (>= 0.7.1) Imports: stats, graphics Suggests: MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate, org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR, BiocStyle License: GPL (>= 2) Package: GSCA Version: 2.34.0 Depends: shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5, R(>= 2.10.0) Imports: graphics Suggests: Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr License: GPL (>= 2) Package: gscreend Version: 1.18.0 Depends: R (>= 3.6) Imports: SummarizedExperiment, nloptr, fGarch, methods, BiocParallel, graphics Suggests: knitr, testthat, rmarkdown, BiocStyle License: GPL-3 Package: GSEABase Version: 1.66.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.13.8), Biobase (>= 2.17.8), annotate (>= 1.45.3), methods, graph (>= 1.37.2) Imports: AnnotationDbi, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools, testthat, BiocStyle, knitr, RUnit License: Artistic-2.0 Package: GSEABenchmarkeR Version: 1.24.0 Depends: R (>= 3.5.0), Biobase, SummarizedExperiment Imports: AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, S4Vectors, stats, utils Suggests: BiocStyle, GSE62944, knitr, rappdirs, rmarkdown License: Artistic-2.0 Package: GSEAlm Version: 1.64.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 Package: GSEAmining Version: 1.14.0 Depends: R (>= 4.0) Imports: dplyr, tidytext, dendextend, tibble, ggplot2, ggwordcloud, stringr, gridExtra, rlang, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, clusterProfiler, testthat, tm License: GPL-3 | file LICENSE Package: gsean Version: 1.24.0 Depends: R (>= 3.5), fgsea, PPInfer Suggests: SummarizedExperiment, pasilla, org.Dm.eg.db, AnnotationDbi, knitr, plotly, WGCNA, rmarkdown License: Artistic-2.0 Archs: x64 Package: GSgalgoR Version: 1.14.0 Imports: cluster, doParallel, foreach, matchingR, nsga2R, survival, proxy, stats, methods, Suggests: knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp, Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP, iC10TrainingData, pamr, testthat License: MIT + file LICENSE Package: GSReg Version: 1.38.0 Depends: R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures, AnnotationDbi Suggests: GenomicRanges, GSBenchMark License: GPL-2 Archs: x64 Package: GSRI Version: 2.52.0 Depends: R (>= 2.14.2), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: parallel License: GPL-3 Package: GSVA Version: 1.52.3 Depends: R (>= 3.5.0) Imports: methods, stats, utils, graphics, S4Vectors, IRanges, Biobase, SummarizedExperiment, GSEABase, Matrix (>= 1.5-0), parallel, BiocParallel, SingleCellExperiment, SpatialExperiment, sparseMatrixStats, DelayedArray, DelayedMatrixStats, HDF5Array, BiocSingular Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinydashboard, ggplot2, data.table, plotly, future, promises, shinybusy, shinyjs License: GPL (>= 2) Archs: x64 Package: gtrellis Version: 1.36.0 Depends: R (>= 3.1.2), grid, IRanges, GenomicRanges Imports: circlize (>= 0.4.8), GetoptLong, grDevices, utils Suggests: testthat (>= 1.0.0), knitr, RColorBrewer, markdown, rmarkdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff License: MIT + file LICENSE Package: GUIDEseq Version: 1.34.0 Depends: R (>= 3.5.0), GenomicRanges, BiocGenerics Imports: Biostrings, pwalign, CRISPRseek, ChIPpeakAnno, data.table, matrixStats, BSgenome, parallel, IRanges (>= 2.5.5), S4Vectors (>= 0.9.6), stringr, multtest, GenomicAlignments (>= 1.7.3), GenomeInfoDb, Rsamtools, hash, limma,dplyr, GenomicFeatures, rio, tidyr, tools, methods, purrr, ggplot2, openxlsx, patchwork, rlang Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) License: GPL (>= 2) Package: Guitar Version: 2.20.0 Depends: GenomicFeatures, rtracklayer,AnnotationDbi, GenomicRanges, magrittr, ggplot2, methods, stats,utils ,knitr,dplyr License: GPL-2 Package: Gviz Version: 1.48.0 Depends: R (>= 4.3), methods, S4Vectors (>= 0.9.25), IRanges (>= 1.99.18), GenomicRanges (>= 1.17.20), grid Imports: XVector (>= 0.5.7), rtracklayer (>= 1.25.13), lattice, RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>= 1.27.5), Biobase (>= 2.15.3), GenomicFeatures (>= 1.17.22), ensembldb (>= 2.11.3), BSgenome (>= 1.33.1), Biostrings (>= 2.33.11), biovizBase (>= 1.13.8), Rsamtools (>= 1.17.28), latticeExtra (>= 0.6-26), matrixStats (>= 0.8.14), GenomicAlignments (>= 1.1.16), GenomeInfoDb (>= 1.1.3), BiocGenerics (>= 0.11.3), digest(>= 0.6.8), graphics, grDevices, stats, utils Suggests: BSgenome.Hsapiens.UCSC.hg19, xml2, BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 Package: GWAS.BAYES Version: 1.14.0 Depends: R (>= 4.3.0) Imports: GA (>= 3.2), caret (>= 6.0-86), memoise (>= 1.1.0), Matrix (>= 1.2-18), limma (>= 3.54.0), stats (>= 4.2.2), MASS (>= 7.3-58.1) Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP License: GPL-3 + file LICENSE Package: gwascat Version: 2.36.0 Depends: R (>= 3.5.0), methods Imports: S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges (>= 1.29.6), GenomicFeatures, readr, Biostrings, AnnotationDbi, BiocFileCache, snpStats, VariantAnnotation, AnnotationHub Suggests: DO.db, DT, knitr, RBGL, testthat, rmarkdown, dplyr, Gviz, Rsamtools, rtracklayer, graph, ggbio, DelayedArray, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BiocStyle Enhances: SNPlocs.Hsapiens.dbSNP144.GRCh37 License: Artistic-2.0 Package: GWASTools Version: 1.50.0 Depends: Biobase Imports: graphics, stats, utils, methods, gdsfmt, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf, quantsmooth, data.table Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel, BiocStyle, knitr License: Artistic-2.0 Package: gwasurvivr Version: 1.22.0 Depends: R (>= 3.4.0) Imports: GWASTools, survival, VariantAnnotation, parallel, matrixStats, SummarizedExperiment, stats, utils, SNPRelate Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 Package: GWENA Version: 1.14.0 Depends: R (>= 4.1) Imports: WGCNA (>= 1.67), dplyr (>= 0.8.3), dynamicTreeCut (>= 1.63-1), ggplot2 (>= 3.1.1), gprofiler2 (>= 0.1.6), magrittr (>= 1.5), tibble (>= 2.1.1), tidyr (>= 1.0.0), NetRep (>= 1.2.1), igraph (>= 1.2.4.1), RColorBrewer (>= 1.1-2), purrr (>= 0.3.3), rlist (>= 0.4.6.1), matrixStats (>= 0.55.0), SummarizedExperiment (>= 1.14.1), stringr (>= 1.4.0), cluster (>= 2.1.0), grDevices (>= 4.0.4), methods, graphics, stats, utils Suggests: testthat (>= 2.1.0), knitr (>= 1.25), rmarkdown (>= 1.16), prettydoc (>= 0.3.0), httr (>= 1.4.1), S4Vectors (>= 0.22.1), BiocStyle (>= 2.15.8) License: GPL-3 Package: gypsum Version: 1.0.1 Imports: utils, tools, httr2, jsonlite, parallel, filelock Suggests: knitr, rmarkdown, testthat, BiocStyle, digest, jsonvalidate, DBI, RSQLite, S4Vectors, methods License: MIT + file LICENSE Package: h5vc Version: 2.38.0 Depends: grid, gridExtra, ggplot2 Imports: rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools (>= 2.13.1), methods, GenomicRanges, abind, BiocParallel, BatchJobs, h5vcData, GenomeInfoDb LinkingTo: Rhtslib (>= 1.99.1) Suggests: knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics, rmarkdown License: GPL (>= 3) Archs: x64 Package: hapFabia Version: 1.46.0 Depends: R (>= 3.6.0), Biobase, fabia (>= 2.3.1) Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) Archs: x64 Package: Harman Version: 1.32.0 Depends: R (>= 3.6) Imports: Rcpp (>= 0.11.2), graphics, stats, Ckmeans.1d.dp, parallel, methods, matrixStats LinkingTo: Rcpp Suggests: HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva License: GPL-3 + file LICENCE Archs: x64 Package: HarmonizR Version: 1.2.0 Depends: R (>= 4.2.0) Imports: doParallel (>= 1.0.16), foreach (>= 1.5.1), janitor (>= 2.1.0), plyr (>= 1.8.6), sva (>= 3.36.0), seriation (>= 1.3.5), limma (>= 3.46.0), SummarizedExperiment Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 Package: Harshlight Version: 1.76.0 Depends: R (>= 2.10) Imports: affy, altcdfenvs, Biobase, stats, utils License: GPL (>= 2) Archs: x64 Package: hca Version: 1.12.0 Depends: R (>= 4.1) Imports: httr, jsonlite, dplyr, tibble, tidyr, readr, BiocFileCache, tools, utils, digest, shiny, miniUI, DT Suggests: LoomExperiment, SummarizedExperiment, SingleCellExperiment, S4Vectors, methods, testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle License: MIT + file LICENSE Package: HDF5Array Version: 1.32.0 Depends: R (>= 3.4), methods, DelayedArray (>= 0.27.2), rhdf5 (>= 2.31.6) Imports: utils, stats, tools, Matrix, rhdf5filters, BiocGenerics (>= 0.31.5), S4Vectors, IRanges, S4Arrays (>= 1.1.1) LinkingTo: S4Vectors (>= 0.27.13), Rhdf5lib Suggests: BiocParallel, GenomicRanges, SummarizedExperiment (>= 1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter, GenomicFeatures, RUnit, SingleCellExperiment, DelayedMatrixStats, genefilter License: Artistic-2.0 Archs: x64 Package: HDTD Version: 1.38.0 Depends: R (>= 4.1) Imports: stats, Rcpp (>= 1.0.1) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown License: GPL-3 Archs: x64 Package: hdxmsqc Version: 1.0.1 Depends: R(>= 4.3), QFeatures, S4Vectors, Spectra Imports: dplyr, tidyr, ggplot2, BiocStyle, knitr, methods, grDevices, stats, MsCoreUtils Suggests: RColorBrewer, pheatmap, MASS, patchwork, testthat License: file LICENSE Package: heatmaps Version: 1.28.0 Depends: R (>= 3.5.0) Imports: methods, grDevices, graphics, stats, Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage, RColorBrewer, BiocGenerics, GenomeInfoDb Suggests: BSgenome.Drerio.UCSC.danRer7, knitr, rmarkdown, testthat License: Artistic-2.0 Package: Heatplus Version: 3.12.0 Imports: graphics, grDevices, stats, RColorBrewer Suggests: Biobase, hgu95av2.db, limma License: GPL (>= 2) Package: HelloRanges Version: 1.30.0 Depends: methods, BiocGenerics, S4Vectors (>= 0.17.39), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.10), Biostrings (>= 2.41.3), BSgenome, GenomicFeatures (>= 1.31.5), VariantAnnotation (>= 1.19.3), Rsamtools, GenomicAlignments (>= 1.15.7), rtracklayer (>= 1.33.8), GenomeInfoDb, SummarizedExperiment, BiocIO Imports: docopt, stats, tools, utils Suggests: HelloRangesData, BiocStyle, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) Package: HELP Version: 1.62.0 Depends: R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods License: GPL (>= 2) Package: HEM Version: 1.76.0 Depends: R (>= 2.1.0) Imports: Biobase, grDevices, stats, utils License: GPL (>= 2) Archs: x64 Package: hermes Version: 1.8.1 Depends: ggfortify, R (>= 4.1), SummarizedExperiment (>= 1.16) Imports: assertthat, Biobase, BiocGenerics, biomaRt, checkmate (>= 2.1), circlize, ComplexHeatmap, DESeq2, dplyr, edgeR, EnvStats, forcats (>= 1.0.0), GenomicRanges, ggplot2, ggrepel (>= 0.9), IRanges, lifecycle, limma, magrittr, matrixStats, methods, MultiAssayExperiment, purrr, R6, Rdpack, rlang, S4Vectors, stats, tidyr, utils Suggests: BiocStyle, DelayedArray, DT, grid, httr, knitr, rmarkdown, statmod, testthat (>= 2.0), vdiffr License: Apache License 2.0 Package: HERON Version: 1.2.0 Depends: R (>= 4.3.0), SummarizedExperiment (>= 1.1.6), GenomicRanges, IRanges, S4Vectors Imports: matrixStats, stats, data.table, harmonicmeanp, metap, cluster, spdep, Matrix, limma, methods Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) Package: HGC Version: 1.12.0 Depends: R (>= 4.1.0) Imports: Rcpp (>= 1.0.0), RcppEigen(>= 0.3.2.0), Matrix, RANN, ape, dendextend, ggplot2, mclust, patchwork, dplyr, grDevices, methods, stats LinkingTo: Rcpp, RcppEigen Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-3 Archs: x64 Package: hiAnnotator Version: 1.38.0 Depends: GenomicRanges, R (>= 2.10) Imports: foreach, iterators, rtracklayer, dplyr, BSgenome, ggplot2, scales, methods Suggests: knitr, doParallel, testthat, BiocGenerics, markdown License: GPL (>= 2) Package: HIBAG Version: 1.40.0 Depends: R (>= 3.2.0) Imports: methods, RcppParallel LinkingTo: RcppParallel (>= 5.0.0) Suggests: parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray, knitr, markdown, rmarkdown, Rsamtools License: GPL-3 Archs: x64 Package: HicAggR Version: 1.0.2 Depends: R (>= 4.2.0) Imports: InteractionSet, BiocGenerics, BiocParallel, dplyr, GenomeInfoDb, GenomicRanges, ggplot2, grDevices, IRanges, Matrix, methods, rhdf5, rlang, rtracklayer, S4Vectors, stats, utils, strawr, tibble, stringr, tidyr, gridExtra, data.table, reshape, checkmate, purrr, withr Suggests: covr, tools, kableExtra (>= 1.3.4), knitr (>= 1.45), rmarkdown, testthat (>= 3.0.0), BiocFileCache (>= 2.6.1) License: MIT + file LICENSE Package: HiCBricks Version: 1.22.0 Depends: R (>= 3.6), utils, curl, rhdf5, R6, grid Imports: ggplot2, viridis, RColorBrewer, scales, reshape2, stringr, data.table, GenomeInfoDb, GenomicRanges, stats, IRanges, grDevices, S4Vectors, digest, tibble, jsonlite, BiocParallel, R.utils, readr, methods Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE Package: HiCcompare Version: 1.26.0 Depends: R (>= 3.5.0), dplyr Imports: data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5 Suggests: knitr, rmarkdown, testthat, multiHiCcompare License: MIT + file LICENSE Package: HiCDCPlus Version: 1.12.0 Imports: Rcpp,InteractionSet,GenomicInteractions,bbmle,pscl,BSgenome,data.table,dplyr,tidyr,GenomeInfoDb,rlang,splines,MASS,GenomicRanges,IRanges,tibble,R.utils,Biostrings,rtracklayer,methods,S4Vectors LinkingTo: Rcpp Suggests: BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, RUnit, BiocGenerics, knitr, rmarkdown, HiTC, DESeq2, Matrix, BiocFileCache, rappdirs Enhances: parallel License: GPL-3 Archs: x64 Package: HiCDOC Version: 1.6.0 Depends: InteractionSet, GenomicRanges, SummarizedExperiment, R (>= 4.1.0) Imports: methods, zlibbioc, ggplot2, Rcpp (>= 0.12.8), stats, S4Vectors, gtools, pbapply, BiocParallel, BiocGenerics, grid, cowplot, gridExtra, data.table, multiHiCcompare, GenomeInfoDb LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, BiocManager, rhdf5 License: LGPL-3 Archs: x64 Package: HiCExperiment Version: 1.4.0 Depends: R (>= 4.2) Imports: InteractionSet, strawr, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, BiocGenerics, BiocIO, BiocParallel, methods, rhdf5, Matrix, vroom, dplyr, stats Suggests: HiContacts, HiContactsData, BiocFileCache, rtracklayer, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE Package: HiContacts Version: 1.6.0 Depends: R (>= 4.2), HiCExperiment Imports: InteractionSet, SummarizedExperiment, GenomicRanges, IRanges, GenomeInfoDb, S4Vectors, methods, BiocGenerics, BiocIO, BiocParallel, RSpectra, Matrix, tibble, tidyr, dplyr, readr, stringr, ggplot2, ggrastr, scales, stats, utils Suggests: HiContactsData, rtracklayer, GenomicFeatures, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra, patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE Package: hicVennDiagram Version: 1.2.0 Depends: R (>= 4.3.0) Imports: GenomeInfoDb, GenomicRanges, IRanges, InteractionSet, rtracklayer, ggplot2, ComplexUpset, reshape2, eulerr, S4Vectors, methods, utils, htmlwidgets, svglite Suggests: BiocStyle, knitr, rmarkdown, testthat, ChIPpeakAnno, grid, TxDb.Hsapiens.UCSC.hg38.knownGene License: GPL-3 Package: hierGWAS Version: 1.34.0 Depends: R (>= 3.2.0) Imports: fastcluster,glmnet, fmsb Suggests: BiocGenerics, RUnit, MASS License: GPL-3 Package: hierinf Version: 1.22.0 Depends: R (>= 3.6.0) Imports: fmsb, glmnet, methods, parallel, stats Suggests: knitr, MASS, testthat License: GPL-3 | file LICENSE Package: HilbertCurve Version: 1.34.0 Depends: R (>= 3.6.0), grid Imports: methods, utils, HilbertVis, png, grDevices, circlize (>= 0.3.3), IRanges, GenomicRanges, polylabelr Suggests: knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0), markdown, RColorBrewer, RCurl, GetoptLong, rmarkdown License: MIT + file LICENSE Package: HilbertVis Version: 1.62.0 Depends: R (>= 2.6.0), grid, lattice Suggests: IRanges, EBImage License: GPL (>= 3) Archs: x64 Package: HiLDA Version: 1.18.0 Depends: R(>= 4.1), ggplot2 Imports: R2jags, abind, cowplot, grid, forcats, stringr, GenomicRanges, S4Vectors, XVector, Biostrings, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, BiocGenerics, tidyr, grDevices, stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 Archs: x64 Package: hipathia Version: 3.4.0 Depends: R (>= 4.1), igraph (>= 1.0.1), AnnotationHub(>= 2.6.5), MultiAssayExperiment(>= 1.4.9), SummarizedExperiment(>= 1.8.1) Imports: coin, stats, limma, grDevices, utils, graphics, preprocessCore, servr, DelayedArray, matrixStats, methods, S4Vectors, ggplot2, ggpubr, dplyr, tibble, visNetwork, reshape2, MetBrewer Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 Package: HIPPO Version: 1.16.0 Depends: R (>= 3.6.0) Imports: ggplot2, graphics, stats, reshape2, gridExtra, Rtsne, umap, dplyr, rlang, magrittr, irlba, Matrix, SingleCellExperiment, ggrepel Suggests: knitr, rmarkdown License: GPL (>= 2) Package: HIREewas Version: 1.22.0 Depends: R (>= 3.5.0) Imports: quadprog, gplots, grDevices, stats Suggests: BiocStyle, knitr, BiocGenerics License: GPL (>= 2) Archs: x64 Package: HiTC Version: 1.48.0 Depends: R (>= 2.15.0), methods, IRanges, GenomicRanges Imports: Biostrings, graphics, grDevices, rtracklayer, RColorBrewer, Matrix, parallel, GenomeInfoDb Suggests: BiocStyle, HiCDataHumanIMR90, BSgenome.Hsapiens.UCSC.hg18 License: Artistic-2.0 Package: hmdbQuery Version: 1.24.0 Depends: R (>= 3.5), XML Imports: S4Vectors, methods, utils Suggests: knitr, annotate, gwascat, testthat, rmarkdown License: Artistic-2.0 Package: HMMcopy Version: 1.46.0 Depends: R (>= 2.10.0), data.table (>= 1.11.8) License: GPL-3 Archs: x64 Package: hoodscanR Version: 1.2.0 Depends: R (>= 4.3) Imports: knitr, rmarkdown, SpatialExperiment, SummarizedExperiment, circlize, ComplexHeatmap, scico, rlang, utils, ggplot2, grid, methods, stats, RANN, Rcpp (>= 1.0.9) LinkingTo: Rcpp Suggests: testthat (>= 3.0.0), BiocStyle License: GPL-3 + file LICENSE Archs: x64 Package: hopach Version: 2.64.0 Depends: R (>= 2.11.0), cluster, Biobase, methods Imports: graphics, grDevices, stats, utils, BiocGenerics License: GPL (>= 2) Archs: x64 Package: HPAanalyze Version: 1.22.0 Depends: R (>= 3.5.0) Imports: dplyr, openxlsx, ggplot2, tibble, xml2, stats, utils, gridExtra Suggests: knitr, rmarkdown, markdown, devtools, BiocStyle License: GPL-3 + file LICENSE Package: hpar Version: 1.46.0 Depends: R (>= 3.5.0) Imports: utils, ExperimentHub Suggests: org.Hs.eg.db, GO.db, AnnotationDbi, knitr, BiocStyle, testthat, rmarkdown, dplyr, DT License: Artistic-2.0 Package: HPiP Version: 1.10.0 Depends: R (>= 4.1) Imports: dplyr (>= 1.0.6), httr (>= 1.4.2), readr, tidyr, tibble, utils, stringr, magrittr, caret, corrplot, ggplot2, pROC, PRROC, igraph, graphics, stats, purrr, grDevices, protr, MCL Suggests: rmarkdown, colorspace, e1071, kernlab, ranger, SummarizedExperiment, Biostrings, randomForest, gprofiler2, gridExtra, ggthemes, BiocStyle, BiocGenerics, RUnit, tools, knitr License: MIT + file LICENSE Package: HTSFilter Version: 1.44.0 Depends: R (>= 4.0.0) Imports: edgeR, DESeq2, BiocParallel, Biobase, utils, stats, grDevices, graphics, methods Suggests: EDASeq, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 Package: HubPub Version: 1.12.0 Imports: available, usethis, biocthis, dplyr, aws.s3, fs, BiocManager, utils Suggests: AnnotationHubData, ExperimentHubData, testthat, knitr, rmarkdown, BiocStyle, License: Artistic-2.0 Package: HumanTranscriptomeCompendium Version: 1.20.0 Depends: R (>= 3.6) Imports: shiny, ssrch, S4Vectors, SummarizedExperiment, utils, BiocManager Suggests: knitr, BiocStyle, beeswarm, tximportData, DT, tximport, dplyr, magrittr, BiocFileCache, testthat, rhdf5client, rmarkdown License: Artistic-2.0 Package: hummingbird Version: 1.14.0 Depends: R (>= 4.0) Imports: Rcpp, graphics, GenomicRanges, SummarizedExperiment, IRanges LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) Archs: x64 Package: HybridExpress Version: 1.0.0 Depends: R (>= 4.3.0) Imports: ggplot2, patchwork, rlang, DESeq2, SummarizedExperiment, stats, methods, RColorBrewer, ComplexHeatmap, grDevices, BiocParallel Suggests: BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0) License: GPL-3 Package: HybridMTest Version: 1.48.0 Depends: R (>= 2.9.0), Biobase, fdrtool, MASS, survival Imports: stats License: GPL (>= 2) Package: hypeR Version: 2.2.0 Depends: R (>= 3.6.0) Imports: ggplot2, ggforce, R6, magrittr, dplyr, purrr, stats, stringr, scales, rlang, httr, openxlsx, htmltools, reshape2, reactable, msigdbr, kableExtra, rmarkdown, igraph, visNetwork, shiny, BiocStyle Suggests: tidyverse, devtools, testthat, knitr License: GPL-3 + file LICENSE Package: hyperdraw Version: 1.56.0 Depends: R (>= 2.9.0) Imports: methods, grid, graph, hypergraph, Rgraphviz, stats4 License: GPL (>= 2) Package: hypergraph Version: 1.76.0 Depends: R (>= 2.1.0), methods, utils, graph Suggests: BiocGenerics, RUnit License: Artistic-2.0 Package: iASeq Version: 1.48.0 Depends: R (>= 2.14.1) Imports: graphics, grDevices License: GPL-2 Package: iasva Version: 1.22.0 Depends: R (>= 3.5), Imports: irlba, stats, cluster, graphics, SummarizedExperiment, BiocParallel Suggests: knitr, testthat, rmarkdown, sva, Rtsne, pheatmap, corrplot, DescTools, RColorBrewer License: GPL-2 Package: iBBiG Version: 1.48.0 Depends: biclust Imports: stats4,xtable,ade4 Suggests: methods License: Artistic-2.0 Archs: x64 Package: ibh Version: 1.52.0 Depends: simpIntLists Suggests: yeastCC, stats License: GPL (>= 2) Package: iBMQ Version: 1.44.0 Depends: R(>= 2.15.0),Biobase (>= 2.16.0), ggplot2 (>= 0.9.2) License: Artistic-2.0 Archs: x64 Package: iCARE Version: 1.32.0 Depends: R (>= 3.3.0), plotrix, gtools, Hmisc Suggests: RUnit, BiocGenerics License: GPL-3 + file LICENSE Archs: x64 Package: Icens Version: 1.76.0 Depends: survival Imports: graphics License: Artistic-2.0 Package: icetea Version: 1.22.0 Depends: R (>= 4.0) Imports: stats, utils, methods, graphics, grDevices, ggplot2, GenomicFeatures, ShortRead, BiocParallel, Biostrings, S4Vectors, Rsamtools, BiocGenerics, IRanges, GenomicAlignments, GenomicRanges, rtracklayer, SummarizedExperiment, VariantAnnotation, limma, edgeR, csaw, DESeq2, TxDb.Dmelanogaster.UCSC.dm6.ensGene Suggests: knitr, rmarkdown, Rsubread (>= 1.29.0), testthat License: GPL-3 + file LICENSE Package: iCheck Version: 1.34.0 Depends: R (>= 3.2.0), Biobase, lumi, gplots Imports: stats, graphics, preprocessCore, grDevices, randomForest, affy, limma, parallel, GeneSelectMMD, rgl, MASS, lmtest, scatterplot3d, utils License: GPL (>= 2) Package: iChip Version: 1.58.0 Depends: R (>= 2.10.0) Imports: limma License: GPL (>= 2) Archs: x64 Package: iClusterPlus Version: 1.40.0 Depends: R (>= 4.1.0), parallel Suggests: RUnit, BiocGenerics License: GPL (>= 2) Archs: x64 Package: iCNV Version: 1.24.0 Depends: R (>= 3.3.1), CODEX Imports: fields, ggplot2, truncnorm, tidyr, data.table, dplyr, grDevices, graphics, stats, utils, rlang Suggests: knitr, rmarkdown, WES.1KG.WUGSC License: GPL-2 Package: iCOBRA Version: 1.32.0 Depends: R (>= 4.4.0) Imports: shiny (>= 0.9.1.9008), shinydashboard, shinyBS, reshape2, ggplot2 (>= 3.4.0), scales, ROCR, dplyr, DT, limma, methods, UpSetR, markdown, utils, rlang Suggests: knitr, rmarkdown, testthat License: GPL (>= 2) Package: ideal Version: 1.28.0 Depends: topGO Imports: DESeq2, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, ggplot2 (>= 2.0.0), heatmaply, plotly, pheatmap, pcaExplorer, IHW, gplots, UpSetR, goseq, stringr, dplyr, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, DT, rentrez, rintrojs, rlang, ggrepel, knitr, rmarkdown, shinyAce, BiocParallel, grDevices, base64enc, methods Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, edgeR License: MIT + file LICENSE Package: IdeoViz Version: 1.40.0 Depends: R (>= 3.5.0), Biobase, IRanges, GenomicRanges, RColorBrewer, rtracklayer, graphics, GenomeInfoDb License: GPL-2 Package: idiogram Version: 1.80.0 Depends: R (>= 2.10), methods, Biobase, annotate, plotrix Suggests: hu6800.db, hgu95av2.db, golubEsets License: GPL-2 Package: idpr Version: 1.14.0 Depends: R (>= 4.1.0) Imports: ggplot2 (>= 3.3.0), magrittr (>= 1.5), dplyr (>= 0.8.5), plyr (>= 1.8.6), jsonlite (>= 1.6.1), rlang (>= 0.4.6), Biostrings (>= 2.56.0), methods (>= 4.0.0) Suggests: knitr, rmarkdown, pwalign, msa, ape, testthat, seqinr License: LGPL (>= 3) Package: idr2d Version: 1.18.0 Depends: R (>= 3.6) Imports: dplyr (>= 0.7.6), futile.logger (>= 1.4.3), GenomeInfoDb (>= 1.14.0), GenomicRanges (>= 1.30), ggplot2 (>= 3.1.1), grDevices, grid, idr (>= 1.2), IRanges (>= 2.18.0), magrittr (>= 1.5), methods, reticulate (>= 1.13), scales (>= 1.0.0), stats, stringr (>= 1.3.1), utils Suggests: DT (>= 0.4), htmltools (>= 0.3.6), knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE Package: IFAA Version: 1.6.0 Depends: R (>= 4.2.0), Imports: mathjaxr, doRNG, foreach (>= 1.4.3), Matrix (>= 1.4-0), HDCI (>= 1.0-2), parallel (>= 3.3.0), doParallel (>= 1.0.11), parallelly , glmnet, stats, utils, SummarizedExperiment, stringr, S4Vectors, DescTools, MatrixExtra, methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle License: GPL-2 Package: iGC Version: 1.34.0 Depends: R (>= 3.2.0) Imports: plyr, data.table Suggests: BiocStyle, knitr, rmarkdown Enhances: doMC License: GPL-2 Package: IgGeneUsage Version: 1.18.0 Depends: R (>= 4.2.0) Imports: methods, reshape2 (>= 1.4.3), Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.2.0), SummarizedExperiment, tidyr LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, ggrepel, patchwork License: MIT + file LICENSE Archs: x64 Package: igvR Version: 1.24.0 Depends: R (>= 3.5.0), GenomicRanges, GenomicAlignments, BrowserViz (>= 2.17.1) Imports: methods, BiocGenerics, httpuv, utils, rtracklayer, VariantAnnotation, RColorBrewer, httr Suggests: RUnit, BiocStyle, knitr, rmarkdown, MotifDb, seqLogo License: MIT + file LICENSE Package: IHW Version: 1.32.0 Depends: R (>= 3.3.0) Imports: methods, slam, lpsymphony, fdrtool, BiocGenerics Suggests: ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat, Matrix, BiocStyle, knitr, rmarkdown, devtools License: Artistic-2.0 Package: illuminaio Version: 0.46.0 Imports: base64 Suggests: RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2), BiocStyle License: GPL-2 Archs: x64 Package: ILoReg Version: 1.14.0 Depends: R (>= 4.0.0) Imports: Matrix, parallel, foreach, aricode, LiblineaR, SparseM, ggplot2, cowplot, RSpectra, umap, Rtsne, fastcluster, parallelDist, cluster, dendextend, DescTools, plyr, scales, pheatmap, reshape2, dplyr, doRNG, SingleCellExperiment, SummarizedExperiment, S4Vectors, methods, stats, doSNOW, utils Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 Package: IMAS Version: 1.28.0 Depends: R (> 3.0.0),GenomicFeatures, ggplot2, IVAS Imports: doParallel, lme4, BiocGenerics, GenomicRanges, IRanges, foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, stats, ggfortify, grDevices, methods, Matrix, utils, graphics, gridExtra, grid, lattice, Rsamtools, survival, BiocParallel, GenomicAlignments, parallel Suggests: BiocStyle, RUnit License: GPL-2 Package: imcRtools Version: 1.10.0 Depends: R (>= 4.1), SpatialExperiment Imports: S4Vectors, stats, utils, SummarizedExperiment, methods, pheatmap, scuttle, stringr, readr, EBImage, cytomapper, abind, BiocParallel, viridis, dplyr, magrittr, DT, igraph, SingleCellExperiment, vroom, BiocNeighbors, RTriangle, ggraph, tidygraph, ggplot2, data.table, sf, concaveman, tidyselect, distances, MatrixGenerics, rlang, grDevices Suggests: CATALYST, grid, tidyr, BiocStyle, knitr, rmarkdown, markdown, testthat License: GPL-3 Package: IMMAN Version: 1.24.0 Imports: STRINGdb, pwalign, igraph, graphics, utils, seqinr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 Package: immunoClust Version: 1.36.0 Depends: R(>= 3.6), flowCore Imports: methods, stats, graphics, grid, lattice, grDevices Suggests: BiocStyle, utils, testthat License: Artistic-2.0 Archs: x64 Package: immunotation Version: 1.12.0 Depends: R (>= 4.1) Imports: stringr, ontologyIndex, curl, ggplot2, readr, rvest, tidyr, xml2, maps, rlang Suggests: BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT License: GPL-3 Package: IMPCdata Version: 1.40.0 Depends: R (>= 2.3.0) Imports: rjson License: file LICENSE Package: impute Version: 1.78.0 Depends: R (>= 2.10) License: GPL-2 Archs: x64 Package: INDEED Version: 2.18.0 Depends: glasso (>= 1.8), R (>= 3.5) Imports: devtools (>= 1.13.0), graphics (>= 3.3.1), stats (>= 3.3.1), utils (>= 3.3.1), igraph (>= 1.2.4), visNetwork(>= 2.0.6) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0) License: Artistic-2.0 Package: iNETgrate Version: 1.2.0 Depends: R (>= 4.3.0), BiocStyle (>= 2.18.1) Imports: SummarizedExperiment, GenomicRanges (>= 1.24.1), stats, WGCNA, grDevices, graphics, survival, igraph, Pigengene (>= 1.19.26), Homo.sapiens, glmnet, caret, gplots, minfi, matrixStats, Rfast, tidyr, tidyselect, utils Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, IlluminaHumanMethylation450kanno.ilmn12.hg19, AnnotationDbi, sesameData, TCGAbiolinks (>= 2.29.4) License: GPL-3 Package: infercnv Version: 1.20.0 Depends: R(>= 4.0) Imports: graphics, grDevices, RColorBrewer, gplots, futile.logger, stats, utils, methods, ape, phyclust, Matrix, fastcluster, parallelDist, dplyr, HiddenMarkov, ggplot2, edgeR, coin, caTools, digest, RANN, igraph, reshape2, rjags, fitdistrplus, future, foreach, doParallel, Seurat, BiocGenerics, SummarizedExperiment, SingleCellExperiment, tidyr, parallel, coda, gridExtra, argparse Suggests: BiocStyle, knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE Package: infinityFlow Version: 1.14.0 Depends: R (>= 4.0.0), flowCore Imports: stats, grDevices, utils, graphics, pbapply, matlab, png, raster, grid, uwot, gtools, Biobase, generics, parallel, methods, xgboost Suggests: knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071 License: GPL-3 Package: Informeasure Version: 1.14.0 Depends: R (>= 4.0) Imports: entropy Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), SummarizedExperiment License: Artistic-2.0 Package: InPAS Version: 2.12.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi,batchtools,Biobase,Biostrings,BSgenome,cleanUpdTSeq, depmixS4,dplyr,flock,future,future.apply,GenomeInfoDb,GenomicRanges, GenomicFeatures, ggplot2, IRanges, limma, magrittr,methods,parallelly, plyranges, preprocessCore, readr,reshape2, RSQLite, stats,S4Vectors, utils Suggests: BiocGenerics,BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, knitr, markdown, rmarkdown, rtracklayer, RUnit, grDevices, TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL (>= 2) Package: INPower Version: 1.40.0 Depends: R (>= 3.1.0), mvtnorm Suggests: RUnit, BiocGenerics License: GPL-2 + file LICENSE Package: INSPEcT Version: 1.34.0 Depends: R (>= 3.6), methods, Biobase, BiocParallel Imports: pROC, deSolve, rootSolve, KernSmooth, readxl, GenomicFeatures, GenomicRanges, IRanges, BiocGenerics, GenomicAlignments, Rsamtools, S4Vectors, GenomeInfoDb, DESeq2, plgem, rtracklayer, SummarizedExperiment, TxDb.Mmusculus.UCSC.mm9.knownGene, shiny Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 Package: INTACT Version: 1.4.0 Depends: R (>= 4.3.0) Imports: SQUAREM, bdsmatrix, numDeriv, stats, tidyr Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 + file LICENSE Package: InTAD Version: 1.24.0 Depends: R (>= 3.5), methods, S4Vectors, IRanges, GenomicRanges, MultiAssayExperiment, SummarizedExperiment,stats Imports: BiocGenerics,Biobase,rtracklayer,parallel,graphics,mclust,qvalue, ggplot2,utils,ggpubr Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL (>= 2) Package: intansv Version: 1.44.0 Depends: R (>= 2.14.0), plyr, ggbio, GenomicRanges Imports: BiocGenerics, IRanges License: MIT + file LICENSE Package: interacCircos Version: 1.14.0 Depends: R (>= 4.1) Imports: RColorBrewer, htmlwidgets, plyr, methods Suggests: knitr, rmarkdown License: GPL-3 Package: InteractionSet Version: 1.32.0 Depends: GenomicRanges, SummarizedExperiment Imports: methods, Matrix, Rcpp, BiocGenerics, S4Vectors (>= 0.27.12), IRanges, GenomeInfoDb LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 Archs: x64 Package: InteractiveComplexHeatmap Version: 1.12.0 Depends: R (>= 4.0.0), ComplexHeatmap (>= 2.11.0) Imports: grDevices, stats, shiny, grid, GetoptLong, S4Vectors (>= 0.26.1), digest, IRanges, kableExtra (>= 1.3.1), utils, svglite, htmltools, clisymbols, jsonlite, RColorBrewer, fontawesome Suggests: knitr, rmarkdown, testthat, EnrichedHeatmap, GenomicRanges, data.table, circlize, GenomicFeatures, tidyverse, tidyHeatmap, cluster, org.Hs.eg.db, simplifyEnrichment, GO.db, SC3, GOexpress, SingleCellExperiment, scater, gplots, pheatmap, airway, DESeq2, DT, cola, BiocManager, gridtext, HilbertCurve (>= 1.21.1), shinydashboard, SummarizedExperiment, pkgndep, ks License: MIT + file LICENSE Package: interactiveDisplay Version: 1.42.0 Depends: R (>= 3.5.0), methods, BiocGenerics, grid Imports: interactiveDisplayBase (>= 1.7.3), shiny, RColorBrewer, ggplot2, reshape2, plyr, gridSVG, XML, Category, AnnotationDbi Suggests: RUnit, hgu95av2.db, knitr, GenomicRanges, SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer, metagenomeSeq, gplots, vegan, Biobase Enhances: rstudio License: Artistic-2.0 Package: interactiveDisplayBase Version: 1.42.0 Depends: R (>= 2.10), methods, BiocGenerics Imports: shiny, DT Suggests: knitr, markdown Enhances: rstudioapi License: Artistic-2.0 Package: InterCellar Version: 2.10.0 Depends: R (>= 4.1) Imports: config, golem, shiny, DT, shinydashboard, shinyFiles, shinycssloaders, data.table, fs, dplyr, tidyr, circlize, colourpicker, dendextend, factoextra, ggplot2, plotly, plyr, shinyFeedback, shinyalert, tibble, umap, visNetwork, wordcloud2, readxl, htmlwidgets, colorspace, signal, scales, htmltools, ComplexHeatmap, grDevices, stats, tools, utils, biomaRt, rlang, fmsb, igraph Suggests: testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite, processx, attempt, BiocStyle, httr License: MIT + file LICENSE Package: IntEREst Version: 1.28.0 Depends: R (>= 3.5.0), GenomicRanges, Rsamtools, SummarizedExperiment, edgeR, S4Vectors, GenomicFiles Imports: seqLogo, Biostrings, GenomicFeatures, txdbmaker, IRanges, seqinr, graphics, grDevices, stats, utils, grid, methods, DBI, RMySQL, GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq, DESeq2 Suggests: clinfun, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-2 Package: InterMineR Version: 1.26.0 Depends: R (>= 3.4.1) Imports: Biostrings, RCurl, XML, xml2, RJSONIO, sqldf, igraph, httr, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, methods Suggests: BiocStyle, Gviz, knitr, rmarkdown, GO.db, org.Hs.eg.db License: LGPL Package: IntramiRExploreR Version: 1.26.0 Depends: R (>= 3.4) Imports: igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats, utils, grDevices, graphics Suggests: gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat License: GPL-2 Package: IONiseR Version: 2.28.0 Depends: R (>= 3.4) Imports: rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2, methods, BiocGenerics, XVector, tibble, stats, BiocParallel, bit64, stringr, utils Suggests: BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData License: MIT + file LICENSE Package: iPAC Version: 1.48.0 Depends: R(>= 2.15), scatterplot3d, Biostrings, pwalign, multtest Imports: grDevices, graphics, stats, gdata License: GPL-2 Package: ipdDb Version: 1.22.0 Depends: R (>= 3.5.0), methods, AnnotationDbi (>= 1.43.1), AnnotationHub Imports: Biostrings, GenomicRanges, RSQLite, DBI, IRanges, stats, assertthat Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 Package: IPO Version: 1.30.0 Depends: xcms (>= 1.50.0), rsm, CAMERA, grDevices, graphics, stats, utils Imports: BiocParallel Suggests: RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr Enhances: parallel License: GPL (>= 2) + file LICENSE Package: IRanges Version: 2.38.1 Depends: R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.39.2), S4Vectors (>= 0.33.3) Imports: stats4 LinkingTo: S4Vectors Suggests: XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle License: Artistic-2.0 Archs: x64 Package: ISAnalytics Version: 1.14.0 Depends: R (>= 4.3) Imports: utils, dplyr, readr, tidyr, purrr, rlang, tibble, stringr, fs, lubridate, lifecycle, ggplot2, ggrepel, stats, readxl, tools, grDevices, forcats, glue, shiny, shinyWidgets, datamods, bslib, DT Suggests: testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown, roxygen2, vegan, withr, extraDistr, ggalluvial, scales, gridExtra, R.utils, RefManageR, flexdashboard, circlize, plotly, gtools, eulerr, openxlsx, jsonlite, pheatmap, BiocParallel, progressr, future, doFuture, foreach, psych, data.table, Rcapture License: CC BY 4.0 Package: iSEE Version: 2.16.0 Depends: SummarizedExperiment, SingleCellExperiment Imports: methods, BiocGenerics, S4Vectors, utils, stats, shiny, shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2, ggrepel, colourpicker, igraph, vipor, mgcv, graphics, grDevices, viridisLite, shinyWidgets, listviewer, ComplexHeatmap, circlize, grid Suggests: testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools License: MIT + file LICENSE Package: iSEEde Version: 1.2.0 Depends: iSEE Imports: DESeq2, edgeR, methods, S4Vectors, shiny, SummarizedExperiment Suggests: airway, BiocStyle, covr, knitr, limma, org.Hs.eg.db, RefManageR, rmarkdown, scuttle, sessioninfo, statmod, testthat (>= 3.0.0) License: Artistic-2.0 Package: iSEEfier Version: 1.0.0 Imports: iSEE, iSEEu, methods, ggplot2, igraph, rlang, stats, SummarizedExperiment, SingleCellExperiment, visNetwork, BiocBaseUtils Suggests: knitr, rmarkdown, scater, scRNAseq, org.Mm.eg.db, scuttle, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE Package: iSEEhex Version: 1.6.0 Depends: SummarizedExperiment, iSEE Imports: ggplot2, hexbin, methods, shiny Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), scRNAseq, scater License: Artistic-2.0 Package: iSEEhub Version: 1.6.0 Depends: SummarizedExperiment, SingleCellExperiment, ExperimentHub Imports: AnnotationHub, BiocManager, DT, iSEE, methods, rintrojs, S4Vectors, shiny, shinydashboard, shinyjs, utils Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), nullrangesData Enhances: BioPlex, biscuiteerData, bodymapRat, CLLmethylation, CopyNeutralIMA, curatedAdipoArray, curatedAdipoChIP, curatedMetagenomicData, curatedTCGAData, DMRcatedata, DuoClustering2018, easierData, emtdata, epimutacionsData, FieldEffectCrc, GenomicDistributionsData, GSE103322, GSE13015, GSE62944, HDCytoData, HMP16SData, HumanAffyData, imcdatasets, mcsurvdata, MetaGxBreast, MetaGxOvarian, MetaGxPancreas, MethylSeqData, muscData, NxtIRFdata, ObMiTi, quantiseqr, restfulSEData, RLHub, sesameData, SimBenchData, SingleCellMultiModal, SingleMoleculeFootprintingData, spatialDmelxsim, STexampleData, TabulaMurisData, TabulaMurisSenisData, TENxVisiumData, tissueTreg, VectraPolarisData, xcoredata License: Artistic-2.0 Package: iSEEindex Version: 1.2.0 Depends: SummarizedExperiment, SingleCellExperiment Imports: BiocFileCache, DT, iSEE, methods, paws.storage, rintrojs, shiny, shinydashboard, shinyjs, stringr, urltools, utils Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), yaml License: Artistic-2.0 Package: iSEEpathways Version: 1.2.0 Depends: iSEE Imports: ggplot2, methods, S4Vectors, shiny, shinyWidgets, stats, SummarizedExperiment Suggests: airway, BiocStyle, covr, edgeR, fgsea, GO.db, iSEEde, knitr, org.Hs.eg.db, RefManageR, rmarkdown, scater, scuttle, sessioninfo, testthat (>= 3.0.0) License: Artistic-2.0 Package: iSEEu Version: 1.16.0 Depends: iSEE, iSEEhex Imports: methods, S4Vectors, IRanges, shiny, SummarizedExperiment, SingleCellExperiment, ggplot2 (>= 3.4.0), DT, stats, colourpicker, shinyAce Suggests: scRNAseq, scater, scran, airway, edgeR, AnnotationDbi, org.Hs.eg.db, GO.db, KEGGREST, knitr, igraph, rmarkdown, BiocStyle, htmltools, Rtsne, uwot, testthat (>= 2.1.0), covr License: MIT + file LICENSE Package: iSeq Version: 1.56.0 Depends: R (>= 2.10.0) License: GPL (>= 2) Archs: x64 Package: ISLET Version: 1.6.0 Depends: R(>= 4.2.0), Matrix, parallel, BiocParallel, SummarizedExperiment, BiocGenerics, lme4, nnls Imports: stats, methods, purrr, abind Suggests: BiocStyle, knitr, rmarkdown, htmltools, RUnit, dplyr License: GPL-2 Package: isobar Version: 1.50.0 Depends: R (>= 2.10.0), Biobase, stats, methods Imports: distr, plyr, biomaRt, ggplot2 Suggests: MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, DBI, MASS License: LGPL-2 Package: IsoBayes Version: 1.2.2 Depends: R (>= 4.3.0) Imports: methods, Rcpp, data.table, glue, stats, doParallel, parallel, doRNG, foreach, iterators, ggplot2,HDInterval, SummarizedExperiment, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 Archs: x64 Package: IsoCorrectoR Version: 1.22.0 Depends: R (>= 3.5) Imports: dplyr, magrittr, methods, quadprog, readr, readxl, stringr, tibble, tools, utils, pracma, WriteXLS Suggests: IsoCorrectoRGUI, knitr, rmarkdown, testthat, BiocStyle License: GPL-3 Package: IsoCorrectoRGUI Version: 1.20.0 Depends: R (>= 3.6) Imports: IsoCorrectoR, readxl, tcltk2, tcltk, utils Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 Package: IsoformSwitchAnalyzeR Version: 2.4.0 Depends: R (>= 4.2), limma, DEXSeq, satuRn (>= 1.7.0), sva, ggplot2 (>= 3.3.5), pfamAnalyzeR Imports: methods, BSgenome, plyr, reshape2, gridExtra, Biostrings (>= 2.50.0), IRanges, GenomicRanges, RColorBrewer, rtracklayer, VennDiagram, DBI, grDevices, graphics, stats, utils, GenomeInfoDb, grid, tximport (>= 1.7.1), tximeta (>= 1.7.12), edgeR, futile.logger, stringr, dplyr, magrittr, readr, tibble, XVector, BiocGenerics, RCurl, Biobase, SummarizedExperiment, tidyr, S4Vectors, BiocParallel, pwalign Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, rmarkdown License: GPL (>= 2) Archs: x64 Package: ISoLDE Version: 1.32.0 Depends: R (>= 3.3.0),graphics,grDevices,stats,utils License: GPL (>= 2.0) Archs: x64 Package: isomiRs Version: 1.32.1 Depends: R (>= 4.4), SummarizedExperiment Imports: AnnotationDbi, BiocGenerics, Biobase, broom, cluster, cowplot, DEGreport, DESeq2, IRanges, dplyr, GenomicRanges, gplots, ggplot2, gtools, gridExtra, grid, grDevices, graphics, GGally, limma, methods, RColorBrewer, readr, reshape, rlang, stats, stringr, S4Vectors, tidyr, tibble Suggests: knitr, rmarkdown, org.Mm.eg.db, targetscan.Hs.eg.db, pheatmap, BiocStyle, testthat License: MIT + file LICENSE Package: ITALICS Version: 2.64.0 Depends: R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser, pd.mapping50k.xba240 Imports: affxparser, DBI, GLAD, oligo, oligoClasses, stats Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp License: GPL-2 Package: iterativeBMA Version: 1.62.0 Depends: BMA, leaps, Biobase (>= 2.5.5) License: GPL (>= 2) Package: iterativeBMAsurv Version: 1.62.0 Depends: BMA, leaps, survival, splines Imports: graphics, grDevices, stats, survival, utils License: GPL (>= 2) Package: iterClust Version: 1.26.0 Depends: R (>= 3.4.1) Imports: Biobase, cluster, stats, methods Suggests: tsne, bcellViper License: file LICENSE Package: IVAS Version: 2.24.0 Depends: R (> 3.0.0),GenomicFeatures, ggplot2, Biobase Imports: doParallel, lme4, BiocGenerics, GenomicRanges, IRanges, foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, ggfortify, grDevices, methods, Matrix, BiocParallel,utils, stats Suggests: BiocStyle License: GPL-2 Package: ivygapSE Version: 1.26.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: shiny, survival, survminer, hwriter, plotly, ggplot2, S4Vectors, graphics, stats, utils, UpSetR Suggests: knitr, png, limma, grid, DT, randomForest, digest, testthat, rmarkdown, BiocStyle, magick, statmod, codetools License: Artistic-2.0 Package: IWTomics Version: 1.28.0 Depends: R (>= 3.5.0), GenomicRanges Imports: parallel,gtable,grid,graphics,methods,IRanges,KernSmooth,fda,S4Vectors,grDevices,stats,utils,tools Suggests: knitr License: GPL (>= 2) Package: karyoploteR Version: 1.30.0 Depends: R (>= 3.4), regioneR, GenomicRanges, methods Imports: regioneR, GenomicRanges, IRanges, Rsamtools, stats, graphics, memoise, rtracklayer, GenomeInfoDb, S4Vectors, biovizBase, digest, bezier, GenomicFeatures, bamsignals, AnnotationDbi, grDevices, VariantAnnotation Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat, magrittr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Hs.eg.db, org.Mm.eg.db, pasillaBamSubset License: Artistic-2.0 Package: katdetectr Version: 1.6.0 Depends: R (>= 4.2) Imports: Biobase (>= 2.54.0), BiocParallel (>= 1.26.2), BSgenome (>= 1.62.0), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.3), BSgenome.Hsapiens.UCSC.hg38 (>= 1.4.4), changepoint (>= 2.2.3), changepoint.np (>= 1.0.3), checkmate (>= 2.0.0), dplyr (>= 1.0.8), GenomeInfoDb (>= 1.28.4), GenomicRanges (>= 1.44.0), ggplot2 (>= 3.3.5), ggtext (>= 0.1.1), IRanges (>= 2.26.0), maftools (>= 2.10.5), methods (>= 4.1.3), plyranges (>= 1.17.0), Rdpack (>= 2.3.1), rlang (>= 1.0.2), S4Vectors (>= 0.30.2), scales (>= 1.2.0), tibble (>= 3.1.6), tidyr (>= 1.2.0), tools, utils, VariantAnnotation (>= 1.38.0) Suggests: BiocStyle (>= 2.26.0), knitr (>= 1.37), rmarkdown (>= 2.13), stats, testthat (>= 3.0.0) License: GPL-3 + file LICENSE Package: KBoost Version: 1.12.0 Depends: R (>= 4.1), stats, utils Suggests: knitr, rmarkdown, testthat License: GPL-2 | GPL-3 Package: KCsmart Version: 2.62.0 Depends: siggenes, multtest, KernSmooth Imports: methods, BiocGenerics Enhances: Biobase, CGHbase License: GPL-3 Package: kebabs Version: 1.38.0 Depends: R (>= 3.3.0), Biostrings (>= 2.35.5), kernlab Imports: methods, stats, Rcpp (>= 0.11.2), Matrix (>= 1.5-0), XVector (>= 0.7.3), S4Vectors (>= 0.27.3), e1071, LiblineaR, graphics, grDevices, utils, apcluster LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors Suggests: SparseM, Biobase, BiocGenerics, knitr License: GPL (>= 2.1) Archs: x64 Package: KEGGgraph Version: 1.64.0 Depends: R (>= 3.5.0) Imports: methods, XML (>= 2.3-0), graph, utils, RCurl, Rgraphviz Suggests: RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db, SPIA License: GPL (>= 2) Package: KEGGlincs Version: 1.30.0 Depends: R (>= 3.3), KOdata, hgu133a.db, org.Hs.eg.db (>= 3.3.0) Imports: AnnotationDbi,KEGGgraph,igraph,plyr,gtools,httr,RJSONIO,KEGGREST, methods,graphics,stats,utils, XML, grDevices Suggests: BiocManager (>= 1.20.3), knitr, graph License: GPL-3 Package: keggorthology Version: 2.56.0 Depends: R (>= 2.5.0),stats,graph,hgu95av2.db Imports: AnnotationDbi,graph,DBI, graph, grDevices, methods, stats, tools, utils Suggests: RBGL,ALL License: Artistic-2.0 Package: KEGGREST Version: 1.44.1 Depends: R (>= 3.5.0) Imports: methods, httr, png, Biostrings Suggests: RUnit, BiocGenerics, knitr, markdown License: Artistic-2.0 Package: KinSwingR Version: 1.22.0 Depends: R (>= 3.5) Imports: data.table, BiocParallel, sqldf, stats, grid, grDevices Suggests: knitr, rmarkdown License: GPL-3 Package: kissDE Version: 1.24.0 Imports: aods3, Biobase, DESeq2, DSS, ggplot2, gplots, graphics, grDevices, matrixStats, stats, utils, foreach, doParallel, parallel, shiny, shinycssloaders, ade4, factoextra, DT Suggests: BiocStyle, testthat License: GPL (>= 2) Package: KnowSeq Version: 1.18.0 Depends: R (>= 4.0), cqn (>= 1.28.1) Imports: stringr, methods, ggplot2 (>= 3.3.0), jsonlite, kernlab, rlist, rmarkdown, reshape2, e1071, randomForest, caret, XML, praznik, R.utils, httr, sva (>= 3.30.1), edgeR (>= 3.24.3), limma (>= 3.38.3), grDevices, graphics, stats, utils, Hmisc (>= 4.4.0), gridExtra Suggests: knitr License: GPL (>= 2) Package: knowYourCG Version: 1.0.0 Depends: R (>= 4.4.0) Imports: sesameData, dplyr, methods, rlang, GenomicRanges, IRanges, reshape2, S4Vectors, stats, stringr, utils Suggests: testthat (>= 3.0.0), SummarizedExperiment, rmarkdown, knitr, sesame, gprofiler2 License: MIT + file LICENSE Package: LACE Version: 2.8.0 Depends: R (>= 4.2.0) Imports: curl, igraph, foreach, doParallel, sortable, dplyr, forcats, data.tree, graphics, grDevices, parallel, RColorBrewer, Rfast, stats, SummarizedExperiment, utils, purrr, stringi, stringr, Matrix, tidyr, jsonlite, readr, configr, DT, tools, fs, data.table, htmltools, htmlwidgets, bsplus, shinyvalidate, shiny, shinythemes, shinyFiles, shinyjs, shinyBS, shinydashboard, biomaRt, callr, logr, ggplot2, svglite Suggests: BiocGenerics, BiocStyle, testthat, knitr, rmarkdown License: file LICENSE Package: lapmix Version: 1.70.0 Depends: R (>= 2.6.0),stats Imports: Biobase, graphics, grDevices, methods, stats, tools, utils License: GPL (>= 2) Package: LBE Version: 1.72.0 Depends: stats Imports: graphics, grDevices, methods, stats, utils Suggests: qvalue License: GPL-2 Package: ldblock Version: 1.34.0 Depends: R (>= 3.5), methods, rlang Imports: BiocGenerics (>= 0.25.1), httr, Matrix Suggests: RUnit, knitr, BiocStyle, gwascat, rmarkdown, snpStats, VariantAnnotation, GenomeInfoDb, ensembldb, EnsDb.Hsapiens.v75, Rsamtools, GenomicFiles (>= 1.13.6) License: Artistic-2.0 Package: LEA Version: 3.16.0 Depends: R (>= 3.3.0), methods, stats, utils, graphics Suggests: knitr License: GPL-3 Archs: x64 Package: LedPred Version: 1.38.0 Depends: R (>= 3.2.0), e1071 (>= 1.6) Imports: akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl, ROCR, testthat License: MIT | file LICENSE Package: lefser Version: 1.14.0 Depends: SummarizedExperiment, R (>= 4.0.0) Imports: coin, MASS, ggplot2, S4Vectors, stats, methods, utils, dplyr Suggests: knitr, rmarkdown, curatedMetagenomicData, BiocStyle, phyloseq, testthat, pkgdown, covr, withr License: Artistic-2.0 Package: lemur Version: 1.2.0 Depends: R (>= 4.1) Imports: stats, utils, irlba, methods, SingleCellExperiment, SummarizedExperiment, rlang, vctrs, glmGamPoi (>= 1.12.0), BiocGenerics, S4Vectors, Matrix, DelayedMatrixStats, HDF5Array, MatrixGenerics, matrixStats, Rcpp, harmony (>= 1.0.3), limma, BiocNeighbors LinkingTo: Rcpp, RcppArmadillo Suggests: testthat (>= 3.0.0), tidyverse, uwot, dplyr, edgeR, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE Archs: x64 Package: les Version: 1.54.0 Depends: R (>= 2.13.2), methods, graphics, fdrtool Imports: boot, gplots, RColorBrewer Suggests: Biobase, limma Enhances: parallel License: GPL-3 Package: levi Version: 1.22.0 Imports: DT(>= 0.4), RColorBrewer(>= 1.1-2), colorspace(>= 1.3-2), dplyr(>= 0.7.4), ggplot2(>= 2.2.1), httr(>= 1.3.1), igraph(>= 1.2.1), reshape2(>= 1.4.3), shiny(>= 1.0.5), shinydashboard(>= 0.7.0), shinyjs(>= 1.0), xml2(>= 1.2.0), knitr, Rcpp (>= 0.12.18), grid, grDevices, stats, utils, testthat, methods, rmarkdown LinkingTo: Rcpp Suggests: rmarkdown, BiocStyle License: GPL (>= 2) Archs: x64 Package: lfa Version: 2.4.0 Depends: R (>= 4.0) Imports: utils, methods, corpcor, RSpectra Suggests: knitr, ggplot2, testthat, BEDMatrix, genio License: GPL (>= 3) Archs: x64 Package: limma Version: 3.60.3 Depends: R (>= 3.6.0) Imports: grDevices, graphics, stats, utils, methods, statmod Suggests: BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines, affy, AnnotationDbi, Biobase, BiocStyle, GO.db, illuminaio, org.Hs.eg.db, vsn License: GPL (>= 2) Archs: x64 Package: limmaGUI Version: 1.80.0 Imports: methods, grDevices, graphics, limma, R2HTML, tcltk, tkrplot, xtable, utils License: GPL (>= 2) Package: limpca Version: 1.0.0 Depends: R (>= 3.5.0) Imports: ggplot2, stringr, plyr, ggrepel, reshape2, grDevices, graphics, doParallel, parallel, dplyr, tibble, tidyr, ggsci, tidyverse, methods, stats, SummarizedExperiment, S4Vectors Suggests: BiocStyle, pander, rmarkdown, car, gridExtra, knitr, testthat (>= 3.0.0) License: Artistic-2.0 Package: lineagespot Version: 1.8.0 Imports: VariantAnnotation, MatrixGenerics, SummarizedExperiment, data.table, stringr, httr, utils Suggests: BiocStyle, RefManageR, rmarkdown, knitr, testthat (>= 3.0.0) License: MIT + file LICENSE Package: LinkHD Version: 1.18.0 Depends: R(>= 3.6.0), methods, ggplot2, stats Imports: scales, cluster, graphics, ggpubr, gridExtra, vegan, rio, MultiAssayExperiment, emmeans, reshape2, data.table Suggests: MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle License: GPL-3 Package: Linnorm Version: 2.28.0 Depends: R(>= 4.1.0) Imports: Rcpp (>= 0.12.2), RcppArmadillo (>= 0.8.100.1.0), fpc, vegan, mclust, apcluster, ggplot2, ellipse, limma, utils, statmod, MASS, igraph, grDevices, graphics, fastcluster, ggdendro, zoo, stats, amap, Rtsne, gmodels LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer, moments, testthat, matrixStats License: MIT + file LICENSE Archs: x64 Package: LinTInd Version: 1.8.0 Depends: R (>= 4.0), ggplot2, parallel, stats, S4Vectors Imports: data.tree, reshape2, networkD3, stringdist, purrr, ape, cowplot, ggnewscale, stringr, dplyr, rlist, pheatmap, Biostrings, pwalign, IRanges, BiocGenerics(>= 0.36.1), ggtree Suggests: knitr, rmarkdown License: MIT + file LICENSE Package: lionessR Version: 1.18.0 Depends: R (>= 3.6.0) Imports: stats, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, igraph, reshape2, limma, License: MIT + file LICENSE Package: lipidr Version: 2.18.0 Depends: R (>= 3.6.0), SummarizedExperiment Imports: methods, stats, utils, data.table, S4Vectors, rlang, dplyr, tidyr, forcats, ggplot2, limma, fgsea, ropls, imputeLCMD, magrittr Suggests: knitr, rmarkdown, BiocStyle, ggrepel, plotly, spelling, testthat License: MIT + file LICENSE Package: LiquidAssociation Version: 1.58.0 Depends: geepack, methods, yeastCC, org.Sc.sgd.db Imports: Biobase, graphics, grDevices, methods, stats License: GPL (>= 3) Package: lisaClust Version: 1.12.1 Depends: R (>= 4.0) Imports: ggplot2, class, concaveman, grid, BiocParallel, spatstat.explore, spatstat.geom, BiocGenerics, S4Vectors, methods, spicyR, purrr, stats, data.table, dplyr, tidyr, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, pheatmap, spatstat.random Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) Package: lmdme Version: 1.46.0 Depends: R (>= 2.14.1), pls, stemHypoxia Imports: stats, methods, limma Enhances: parallel License: GPL (>= 2) Package: LOBSTAHS Version: 1.30.0 Depends: R (>= 3.4), xcms, CAMERA, methods Imports: utils Suggests: PtH2O2lipids, knitr, rmarkdown License: GPL (>= 3) + file LICENSE Package: loci2path Version: 1.24.0 Depends: R (>= 3.5.0) Imports: pheatmap, wordcloud, RColorBrewer, data.table, methods, grDevices, stats, graphics, GenomicRanges, BiocParallel, S4Vectors Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 Package: logicFS Version: 2.24.0 Depends: LogicReg, mcbiopi, survival Imports: graphics, methods, stats Suggests: genefilter, siggenes License: LGPL (>= 2) Package: LOLA Version: 1.34.0 Depends: R (>= 3.5.0) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, reshape2, utils, stats, methods Suggests: parallel, testthat, knitr, BiocStyle, rmarkdown Enhances: simpleCache, qvalue, ggplot2 License: GPL-3 Package: LoomExperiment Version: 1.22.0 Depends: R (>= 3.5.0), S4Vectors, SingleCellExperiment, SummarizedExperiment, methods, rhdf5, BiocIO Imports: DelayedArray, GenomicRanges, HDF5Array, Matrix, stats, stringr, utils Suggests: testthat, BiocStyle, knitr, rmarkdown, reticulate License: Artistic-2.0 Package: LPE Version: 1.78.0 Depends: R (>= 2.10) Imports: stats License: LGPL Package: lpNet Version: 2.36.0 Depends: lpSolve, KEGGgraph License: Artistic License 2.0 Package: lpsymphony Version: 1.32.0 Depends: R (>= 3.0.0) Suggests: BiocStyle, knitr, testthat Enhances: slam License: EPL Archs: x64 Package: LRBaseDbi Version: 2.14.0 Depends: R (>= 3.5.0) Imports: methods, stats, utils, AnnotationDbi, RSQLite, DBI, Biobase Suggests: testthat, BiocStyle, AnnotationHub License: Artistic-2.0 Package: LRcell Version: 1.12.0 Depends: R (>= 4.1), ExperimentHub, AnnotationHub Imports: BiocParallel, dplyr, ggplot2, ggrepel, magrittr, stats, utils Suggests: LRcellTypeMarkers, BiocStyle, knitr, rmarkdown, roxygen2, testthat License: MIT + file LICENSE Package: lumi Version: 2.56.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Imports: affy (>= 1.23.4), methylumi (>= 2.3.2), GenomicFeatures, GenomicRanges, annotate, lattice, mgcv (>= 1.4-0), nleqslv, KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS, graphics, stats, stats4, methods Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer License: LGPL (>= 2) Package: lute Version: 1.0.0 Depends: R (>= 4.3.0), stats, methods, utils, SummarizedExperiment, SingleCellExperiment, BiocGenerics Imports: S4Vectors, Biobase, scran, dplyr, ggplot2 Suggests: nnls, knitr, testthat, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub, DelayedMatrixStats, BisqueRNA, DelayedArray License: Artistic-2.0 Package: LymphoSeq Version: 1.32.0 Depends: R (>= 3.3), LymphoSeqDB Imports: data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq, RColorBrewer, circlize, grid, utils, stats, ggtree, msa, Biostrings, phangorn, stringdist, UpSetR Suggests: knitr, pheatmap, wordcloud, rmarkdown License: Artistic-2.0 Package: M3C Version: 1.26.0 Depends: R (>= 3.5.0) Imports: ggplot2, Matrix, doSNOW, cluster, parallel, foreach, doParallel, matrixcalc, Rtsne, corpcor, umap Suggests: knitr, rmarkdown License: AGPL-3 Package: M3Drop Version: 1.30.0 Depends: R (>= 3.4), numDeriv Imports: RColorBrewer, gplots, bbmle, statmod, grDevices, graphics, stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods, scater Suggests: ROCR, knitr, M3DExampleData, SingleCellExperiment, Seurat, Biobase License: GPL (>= 2) Package: m6Aboost Version: 1.10.0 Depends: S4Vectors, adabag, GenomicRanges, R (>= 4.1) Imports: dplyr, rtracklayer, BSgenome, Biostrings, utils, methods, IRanges, ExperimentHub Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 Package: Maaslin2 Version: 1.18.0 Depends: R (>= 3.6) Imports: robustbase, biglm, pcaPP, edgeR, metagenomeSeq, pbapply, car, dplyr, vegan, chemometrics, ggplot2, pheatmap, logging, data.table, lmerTest, hash, optparse, grDevices, stats, utils, glmmTMB, MASS, cplm, pscl, lme4, tibble Suggests: knitr, testthat (>= 2.1.0), rmarkdown, markdown License: MIT + file LICENSE Package: Macarron Version: 1.8.1 Depends: R (>= 4.2.0), SummarizedExperiment Imports: BiocParallel, DelayedArray, WGCNA, ff, data.table, dynamicTreeCut, Maaslin2, plyr, stats, psych, xml2, httr, RJSONIO, logging, methods, utils Suggests: knitr, BiocStyle, optparse, testthat (>= 2.1.0), rmarkdown, markdown License: MIT + file LICENSE Package: maCorrPlot Version: 1.74.0 Depends: lattice Imports: graphics, grDevices, lattice, stats License: GPL (>= 2) Package: MACSQuantifyR Version: 1.18.0 Imports: readxl, graphics, tools, utils, grDevices, ggplot2, ggrepel, methods, stats, latticeExtra, lattice, rmarkdown, png, grid, gridExtra, prettydoc, rvest, xml2 Suggests: knitr, testthat, R.utils, spelling License: Artistic-2.0 Package: made4 Version: 1.78.0 Depends: RColorBrewer,gplots,scatterplot3d, Biobase, SummarizedExperiment Imports: ade4 Suggests: affy, BiocStyle, knitr, rmarkdown License: Artistic-2.0 Package: MADSEQ Version: 1.30.0 Depends: R (>= 3.5.0), rjags (>= 4.6) Imports: VGAM, coda, BSgenome, BSgenome.Hsapiens.UCSC.hg19, S4Vectors, methods, preprocessCore, GenomicAlignments, Rsamtools, Biostrings, GenomicRanges, IRanges, VariantAnnotation, SummarizedExperiment, GenomeInfoDb, rtracklayer, graphics, stats, grDevices, utils, zlibbioc, vcfR Suggests: knitr License: GPL (>= 2) Package: maftools Version: 2.20.0 Depends: R (>= 3.3) Imports: data.table, grDevices, methods, RColorBrewer, Rhtslib, survival, DNAcopy LinkingTo: Rhtslib, zlibbioc Suggests: berryFunctions, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr, mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment, rmarkdown, S4Vectors, pheatmap, curl License: MIT + file LICENSE Archs: x64 Package: MAGAR Version: 1.12.0 Depends: R (>= 4.1), HDF5Array, RnBeads, snpStats, crlmm Imports: doParallel, igraph, bigstatsr, rjson, plyr, data.table, UpSetR, reshape2, jsonlite, methods, ff, argparse, impute, RnBeads.hg19, RnBeads.hg38, utils, stats Suggests: gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil, rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools, BiocGenerics, BiocManager License: GPL-3 Package: MAGeCKFlute Version: 2.8.0 Depends: R (>= 4.1) Imports: Biobase, gridExtra, ggplot2, ggrepel, grDevices, grid, reshape2, stats, utils, DOSE, clusterProfiler, pathview, enrichplot, msigdbr, depmap Suggests: biomaRt, BiocStyle, dendextend, graphics, knitr, pheatmap, png, scales, sva, BiocManager License: GPL (>= 3) Package: magpie Version: 1.4.0 Depends: R (>= 4.3.0) Imports: utils, rtracklayer, Matrix, matrixStats, stats, S4Vectors, methods, graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools, AnnotationDbi, aod, BiocParallel, DESeq2, openxlsx, RColorBrewer, reshape2, TRESS Suggests: knitr, rmarkdown, kableExtra, RUnit, TBX20BamSubset, BiocGenerics, BiocStyle License: MIT + file LICENSE Package: magrene Version: 1.6.0 Depends: R (>= 4.2.0) Imports: utils, stats, BiocParallel Suggests: BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo, testthat (>= 3.0.0) License: GPL-3 Package: MAI Version: 1.10.0 Depends: R (>= 3.5.0) Imports: caret, parallel, doParallel, foreach, e1071, future.apply, future, missForest, pcaMethods, tidyverse, stats, utils, methods, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 Package: maigesPack Version: 1.68.0 Depends: R (>= 2.10), convert, graph, limma, marray, methods Suggests: amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML, rgl, som License: GPL (>= 2) Archs: x64 Package: MAIT Version: 1.38.0 Depends: R (>= 2.10), CAMERA, Rcpp, pls Imports: gplots,e1071,class,MASS,plsgenomics,agricolae,xcms,methods,caret Suggests: faahKO Enhances: rgl License: GPL-2 Package: makecdfenv Version: 1.80.0 Depends: R (>= 2.6.0), affyio Imports: Biobase, affy, methods, stats, utils, zlibbioc License: GPL (>= 2) Archs: x64 Package: MANOR Version: 1.76.0 Depends: R (>= 2.10) Imports: GLAD, graphics, grDevices, stats, utils Suggests: knitr, rmarkdown, bookdown License: GPL-2 Archs: x64 Package: MantelCorr Version: 1.74.0 Depends: R (>= 2.10) Imports: stats License: GPL (>= 2) Package: MAPFX Version: 1.0.0 Depends: R (>= 4.4.0) Imports: flowCore, Biobase, stringr, uwot, iCellR, igraph, ggplot2, RColorBrewer, Rfast, ComplexHeatmap, circlize, glmnetUtils, e1071, xgboost, parallel, pbapply, reshape2, gtools, utils, stats, cowplot, methods, grDevices, graphics Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 Package: maPredictDSC Version: 1.42.0 Depends: R (>= 2.15.0), MASS,affy,limma,gcrma,ROC,class,e1071,caret,hgu133plus2.db,ROCR,AnnotationDbi,LungCancerACvsSCCGEO Suggests: parallel License: GPL-2 Package: mapscape Version: 1.28.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), base64enc (>= 0.1-3), stringr (>= 1.0.0) Suggests: knitr, rmarkdown License: GPL-3 Package: mariner Version: 1.4.0 Depends: R (>= 4.2.0) Imports: methods, S4Vectors, BiocGenerics, BiocManager, GenomicRanges, InteractionSet, data.table, stats, rlang, glue, assertthat, plyranges, magrittr, dbscan, purrr, progress, GenomeInfoDb, strawr (>= 0.0.91), DelayedArray, HDF5Array, abind, BiocParallel, IRanges, SummarizedExperiment, rhdf5, plotgardener, RColorBrewer, colourvalues, utils, grDevices, graphics, grid Suggests: knitr, testthat (>= 3.0.0), dplyr, rmarkdown, ExperimentHub, marinerData License: GPL-3 Package: marr Version: 1.14.0 Depends: R (>= 4.0) Imports: Rcpp, SummarizedExperiment, utils, methods, ggplot2, dplyr, magrittr, rlang, S4Vectors LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, covr License: GPL (>= 3) Archs: x64 Package: marray Version: 1.82.0 Depends: R (>= 2.10.0), limma, methods Suggests: tkWidgets License: LGPL Package: martini Version: 1.24.0 Depends: R (>= 4.0) Imports: igraph (>= 1.0.1), Matrix, memoise (>= 2.0.0), methods (>= 3.3.2), Rcpp (>= 0.12.8), snpStats (>= 1.20.0), stats, utils, LinkingTo: Rcpp, RcppEigen (>= 0.3.3.5.0) Suggests: biomaRt (>= 2.34.1), circlize (>= 0.4.11), STRINGdb (>= 2.2.0), httr (>= 1.2.1), IRanges (>= 2.8.2), S4Vectors (>= 0.12.2), knitr, testthat, readr, rmarkdown License: GPL-3 Archs: x64 Package: maser Version: 1.22.0 Depends: R (>= 3.5.0), ggplot2, GenomicRanges Imports: dplyr, rtracklayer, reshape2, Gviz, DT, GenomeInfoDb, stats, utils, IRanges, methods, BiocGenerics, parallel, data.table Suggests: testthat, knitr, rmarkdown, BiocStyle, AnnotationHub License: MIT + file LICENSE Package: maSigPro Version: 1.76.0 Depends: R (>= 2.3.1) Imports: Biobase, graphics, grDevices, venn, mclust, stats, MASS License: GPL (>= 2) Package: maskBAD Version: 1.48.0 Depends: R (>= 2.10), gcrma (>= 2.27.1), affy Suggests: hgu95av2probe, hgu95av2cdf License: GPL (>= 2) Package: MassArray Version: 1.56.0 Depends: R (>= 2.10.0), methods Imports: graphics, grDevices, stats, utils License: GPL (>= 2) Package: massiR Version: 1.40.0 Depends: cluster, gplots, diptest, Biobase, R (>= 3.0.2) Suggests: biomaRt, RUnit, BiocGenerics License: GPL-3 Package: MassSpecWavelet Version: 1.70.0 Suggests: signal, waveslim, BiocStyle, knitr, rmarkdown, RUnit, bench License: LGPL (>= 2) Archs: x64 Package: MAST Version: 1.30.0 Depends: SingleCellExperiment (>= 1.2.0), R(>= 3.5) Imports: Biobase, BiocGenerics, S4Vectors, data.table, ggplot2, plyr, stringr, abind, methods, parallel, reshape2, stats, stats4, graphics, utils, SummarizedExperiment(>= 1.5.3), progress, Matrix Suggests: knitr, rmarkdown, testthat, lme4(>= 1.0), blme, roxygen2(> 6.0.0), numDeriv, car, gdata, lattice, GGally, GSEABase, NMF, TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer, BiocStyle, scater, DelayedArray, HDF5Array, zinbwave, dplyr License: GPL (>= 2) Package: mastR Version: 1.4.0 Depends: R (>= 4.3.0) Imports: AnnotationDbi, Biobase, dplyr, edgeR, ggplot2, ggpubr, graphics, grDevices, GSEABase, limma, Matrix, methods, msigdb, org.Hs.eg.db, patchwork, SeuratObject, SingleCellExperiment, stats, SummarizedExperiment, tidyr, utils Suggests: BiocManager, BiocStyle, BisqueRNA, clusterProfiler, ComplexHeatmap, depmap, enrichplot, ggrepel, ggvenn, gridExtra, jsonlite, knitr, rmarkdown, RobustRankAggreg, rvest, scuttle, singscore, splatter, testthat (>= 3.0.0), UpSetR License: MIT + file LICENSE Package: matchBox Version: 1.46.0 Depends: R (>= 2.8.0) License: Artistic-2.0 Package: MatrixGenerics Version: 1.16.0 Depends: matrixStats (>= 1.0.0) Imports: methods Suggests: Matrix, sparseMatrixStats, SparseArray, DelayedArray, DelayedMatrixStats, SummarizedExperiment, testthat (>= 2.1.0) License: Artistic-2.0 Package: MatrixQCvis Version: 1.12.0 Depends: SummarizedExperiment (>= 1.20.0), plotly (>= 4.9.3), shiny (>= 1.6.0) Imports: ComplexHeatmap (>= 2.7.9), dplyr (>= 1.0.5), ExperimentHub (>= 2.6.0), ggplot2 (>= 3.3.3), grDevices (>= 4.1.0), Hmisc (>= 4.5-0), htmlwidgets (>= 1.5.3), impute (>= 1.65.0), imputeLCMD (>= 2.0), limma (>= 3.47.12), MASS (>= 7.3-58.1), methods (>= 4.1.0), pcaMethods (>= 1.83.0), proDA (>= 1.5.0), rlang (>= 0.4.10), rmarkdown (>= 2.7), Rtsne (>= 0.15), shinydashboard (>= 0.7.1), shinyhelper (>= 0.3.2), shinyjs (>= 2.0.0), stats (>= 4.1.0), tibble (>= 3.1.1), tidyr (>= 1.1.3), umap (>= 0.2.7.0), UpSetR (>= 1.4.0), vsn (>= 3.59.1) Suggests: BiocGenerics (>= 0.37.4), BiocStyle (>= 2.19.2), hexbin (>= 1.28.2), httr (>= 1.4.7), jpeg (>= 0.1-10), knitr (>= 1.33), statmod (>= 1.5.0), testthat (>= 3.0.2) License: GPL-3 Package: MatrixRider Version: 1.36.0 Depends: R (>= 3.1.2) Imports: methods, TFBSTools, IRanges, XVector, Biostrings LinkingTo: IRanges, XVector, Biostrings, S4Vectors Suggests: RUnit, BiocGenerics, BiocStyle, JASPAR2014 License: GPL-3 Archs: x64 Package: matter Version: 2.6.2 Depends: R (>= 4.0), BiocParallel, Matrix, methods Imports: BiocGenerics, ProtGenerics, digest, irlba, biglm, stats, stats4, graphics, grDevices, utils Suggests: BiocStyle, knitr, testthat, plotly License: Artistic-2.0 Archs: x64 Package: MBAmethyl Version: 1.38.0 Depends: R (>= 2.15) License: Artistic-2.0 Package: MBASED Version: 1.38.0 Depends: RUnit, BiocGenerics, BiocParallel, GenomicRanges, SummarizedExperiment Suggests: BiocStyle License: Artistic-2.0 Package: MBCB Version: 1.58.0 Depends: R (>= 2.9.0), tcltk, tcltk2 Imports: preprocessCore, stats, utils License: GPL (>= 2) Package: MBECS Version: 1.8.0 Depends: R (>= 4.1) Imports: methods, magrittr, phyloseq, limma, lme4, lmerTest, pheatmap, rmarkdown, cluster, dplyr, ggplot2, gridExtra, ruv, sva, tibble, tidyr, vegan, stats, utils, Matrix Suggests: knitr, markdown, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 Package: mbkmeans Version: 1.20.0 Depends: R (>= 3.6) Imports: methods, DelayedArray, Rcpp, S4Vectors, SingleCellExperiment, SummarizedExperiment, ClusterR, benchmarkme, Matrix, BiocParallel LinkingTo: Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR Suggests: beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData, scater, DelayedMatrixStats, bluster, knitr, testthat, rmarkdown License: MIT + file LICENSE Archs: x64 Package: mBPCR Version: 1.58.0 Depends: oligoClasses, GWASTools Imports: Biobase, graphics, methods, utils, grDevices Suggests: xtable License: GPL (>= 2) Package: MBQN Version: 2.16.0 Depends: R (>= 3.6) Imports: stats, graphics, utils, limma (>= 3.30.13), SummarizedExperiment (>= 1.10.0), preprocessCore (>= 1.36.0), BiocFileCache, rappdirs, xml2, RCurl, ggplot2, PairedData, rmarkdown Suggests: knitr License: GPL-3 + file LICENSE Package: mbQTL Version: 1.4.0 Depends: R (>= 4.3.0) Imports: MatrixEQTL, dplyr, ggplot2, readxl, stringr, tidyr, metagenomeSeq, pheatmap, broom, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE Package: MBttest Version: 1.32.0 Depends: R (>= 3.3.0), stats, gplots, gtools,graphics,base, utils,grDevices Suggests: BiocStyle, BiocGenerics License: GPL-3 Package: MCbiclust Version: 1.28.0 Depends: R (>= 3.4) Imports: BiocParallel, graphics, utils, stats, AnnotationDbi, GO.db, org.Hs.eg.db, GGally, ggplot2, scales, cluster, WGCNA Suggests: gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr, pander, devtools, testthat, GSVA License: GPL-2 Package: mCSEA Version: 1.24.0 Depends: R (>= 3.5), mCSEAdata, Homo.sapiens Imports: biomaRt, fgsea, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, Gviz, IRanges, limma, methods, parallel, S4Vectors, stats, SummarizedExperiment, utils Suggests: Biobase, BiocGenerics, BiocStyle, FlowSorted.Blood.450k, knitr, leukemiasEset, minfi, minfiData, rmarkdown, RUnit License: GPL-2 Package: mdp Version: 1.24.0 Depends: R (>= 4.0) Imports: ggplot2, gridExtra, grid, stats, utils Suggests: testthat, knitr, rmarkdown, fgsea, BiocManager License: GPL-3 Package: mdqc Version: 1.66.0 Depends: R (>= 2.2.1), cluster, MASS License: LGPL (>= 2) Package: MDTS Version: 1.24.0 Depends: R (>= 3.5.0) Imports: GenomicAlignments, GenomicRanges, IRanges, Biostrings, DNAcopy, Rsamtools, parallel, stringr Suggests: testthat, knitr License: Artistic-2.0 Package: MEAL Version: 1.34.0 Depends: R (>= 3.6.0), Biobase, MultiDataSet Imports: GenomicRanges, limma, vegan, BiocGenerics, minfi, IRanges, S4Vectors, methods, parallel, ggplot2 (>= 2.0.0), permute, Gviz, missMethyl, isva, SummarizedExperiment, SmartSVA, graphics, stats, utils, matrixStats Suggests: testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData, BiocStyle, rmarkdown, brgedata License: Artistic-2.0 Package: MeasurementError.cor Version: 1.76.0 License: LGPL Package: MEAT Version: 1.16.0 Depends: R (>= 4.0) Imports: impute (>= 1.58), dynamicTreeCut (>= 1.63), glmnet (>= 2.0), grDevices, graphics, stats, utils, stringr, tibble, RPMM (>= 1.25), minfi (>= 1.30), dplyr, SummarizedExperiment, wateRmelon Suggests: knitr, markdown, rmarkdown, BiocStyle, testthat (>= 2.1.0) License: MIT + file LICENSE Package: MEB Version: 1.18.0 Depends: R (>= 3.6.0) Imports: e1071, edgeR, scater, stats, wrswoR, SummarizedExperiment, SingleCellExperiment Suggests: knitr,rmarkdown,BiocStyle License: GPL-2 Package: MEDIPS Version: 1.56.0 Depends: R (>= 3.0), BSgenome, Rsamtools Imports: GenomicRanges, Biostrings, graphics, gtools, IRanges, methods, stats, utils, edgeR, DNAcopy, biomaRt, rtracklayer, preprocessCore Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, BiocStyle License: GPL (>= 2) Package: MEDME Version: 1.64.0 Depends: R (>= 2.15), grDevices, graphics, methods, stats, utils Imports: Biostrings, MASS, drc Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9 License: GPL (>= 2) Archs: x64 Package: megadepth Version: 1.14.0 Imports: xfun, utils, fs, GenomicRanges, readr, cmdfun, dplyr, magrittr Suggests: covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer, derfinder, GenomeInfoDb, tools, RefManageR, testthat License: Artistic-2.0 Package: MEIGOR Version: 1.38.0 Depends: R (>= 4.0), Rsolnp, snowfall, deSolve, CNORode Suggests: CellNOptR, knitr, BiocStyle License: GPL-3 Package: Melissa Version: 1.20.0 Depends: R (>= 3.5.0), BPRMeth, GenomicRanges Imports: data.table, parallel, ROCR, matrixcalc, mclust, ggplot2, doParallel, foreach, MCMCpack, cowplot, magrittr, mvtnorm, truncnorm, assertthat, BiocStyle, stats, utils Suggests: testthat, knitr, rmarkdown License: GPL-3 | file LICENSE Package: memes Version: 1.12.0 Depends: R (>= 4.1) Imports: Biostrings, dplyr, cmdfun (>= 1.0.2), GenomicRanges, ggplot2, ggseqlogo, magrittr, matrixStats, methods, patchwork, processx, purrr, rlang, readr, stats, tools, tibble, tidyr, utils, usethis, universalmotif (>= 1.9.3), xml2 Suggests: cowplot, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Dmelanogaster.UCSC.dm6, forcats, testthat (>= 2.1.0), knitr, MotifDb, pheatmap, PMCMRplus, plyranges (>= 1.9.1), rmarkdown, covr License: MIT + file LICENSE Package: Mergeomics Version: 1.32.0 Depends: R (>= 3.0.1) Suggests: RUnit, BiocGenerics License: GPL (>= 2) Package: MeSHDbi Version: 1.40.0 Depends: R (>= 3.0.1) Imports: methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase Suggests: testthat License: Artistic-2.0 Package: meshes Version: 1.30.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, DOSE, enrichplot, GOSemSim, methods, utils, AnnotationHub, MeSHDbi, yulab.utils Suggests: knitr, rmarkdown, prettydoc License: Artistic-2.0 Package: meshr Version: 2.10.0 Depends: R (>= 4.1.0) Imports: markdown, rmarkdown, BiocStyle, knitr, methods, stats, utils, fdrtool, MeSHDbi, Category, S4Vectors, BiocGenerics, RSQLite License: Artistic-2.0 Package: MesKit Version: 1.14.0 Depends: R (>= 4.0.0) Imports: methods, data.table, Biostrings, dplyr, tidyr (>= 1.0.0), ape (>= 5.4.1), ggrepel, pracma, ggridges, AnnotationDbi, IRanges, circlize, cowplot, mclust, phangorn, ComplexHeatmap (>= 1.9.3), ggplot2, RColorBrewer, grDevices, stats, utils, S4Vectors Suggests: shiny, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), org.Hs.eg.db, clusterProfiler, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 Package: messina Version: 1.40.0 Depends: R (>= 3.1.0), survival (>= 2.37-4), methods Imports: Rcpp (>= 0.11.1), plyr (>= 1.8), ggplot2 (>= 0.9.3.1), grid (>= 3.1.0), foreach (>= 1.4.1), graphics LinkingTo: Rcpp Suggests: knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>= 2.22.0), BiocStyle Enhances: doMC (>= 1.3.3) License: EPL (>= 1.0) Archs: x64 Package: metabCombiner Version: 1.14.0 Depends: R (>= 4.0) Imports: dplyr (>= 1.0), methods, mgcv, caret, S4Vectors, stats, utils, rlang, graphics, matrixStats, tidyr Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 Archs: x64 Package: metabinR Version: 1.6.0 Depends: R (>= 4.3) Imports: methods, rJava Suggests: BiocStyle, cvms, data.table, dplyr, ggplot2, gridExtra, knitr, R.utils, rmarkdown, sabre, spelling, testthat (>= 3.0.0) License: GPL-3 Package: MetaboAnnotation Version: 1.8.1 Depends: R (>= 4.0.0) Imports: BiocGenerics, MsCoreUtils, MetaboCoreUtils, ProtGenerics, methods, S4Vectors, Spectra (>= 1.13.2), BiocParallel, SummarizedExperiment, QFeatures, AnnotationHub, graphics, CompoundDb Suggests: testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny, shinyjs, DT, microbenchmark, mzR Enhances: RMariaDB, RSQLite License: Artistic-2.0 Package: MetaboCoreUtils Version: 1.12.0 Depends: R (>= 4.0) Imports: utils, MsCoreUtils, BiocParallel, methods, stats Suggests: BiocStyle, testthat, knitr, rmarkdown, robustbase License: Artistic-2.0 Package: metabolomicsWorkbenchR Version: 1.14.2 Depends: R (>= 4.0) Imports: data.table, httr, jsonlite, methods, MultiAssayExperiment, struct, SummarizedExperiment, utils Suggests: BiocStyle, covr, knitr, HDF5Array, httptest, rmarkdown, structToolbox, testthat, pmp, grid, png License: GPL-3 Package: metabomxtr Version: 1.38.0 Depends: methods,Biobase Imports: optimx, Formula, plyr, multtest, BiocParallel, ggplot2 Suggests: xtable, reshape2 License: GPL-2 Package: MetaboSignal Version: 1.34.0 Depends: R(>= 3.3) Imports: KEGGgraph, hpar, igraph, RCurl, KEGGREST, EnsDb.Hsapiens.v75, stats, graphics, utils, org.Hs.eg.db, biomaRt, AnnotationDbi, MWASTools, mygene Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: GPL-3 Package: metaCCA Version: 1.32.0 Suggests: knitr License: MIT + file LICENSE Package: MetaCyto Version: 1.26.0 Depends: R (>= 3.4) Imports: flowCore (>= 1.4),tidyr (>= 0.7),fastcluster,ggplot2,metafor,cluster,FlowSOM, grDevices, graphics, stats, utils Suggests: knitr, dplyr, rmarkdown License: GPL (>= 2) Package: metagene2 Version: 1.20.0 Depends: R (>= 4.0), R6 (>= 2.0), GenomicRanges, BiocParallel Imports: rtracklayer, tools, GenomicAlignments, GenomeInfoDb, IRanges, ggplot2, Rsamtools, purrr, data.table, methods, dplyr, magrittr, reshape2 Suggests: BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown License: Artistic-2.0 Package: metagene Version: 2.36.0 Depends: R (>= 3.5.0), R6 (>= 2.0), GenomicRanges, BiocParallel Imports: rtracklayer, gplots, tools, GenomicAlignments, GenomeInfoDb, GenomicFeatures, IRanges, ggplot2, Rsamtools, matrixStats, purrr, data.table, magrittr, methods, utils, ensembldb, EnsDb.Hsapiens.v86, stringr Suggests: BiocGenerics, similaRpeak, RUnit, knitr, BiocStyle, rmarkdown License: Artistic-2.0 | file LICENSE Package: metagenomeSeq Version: 1.46.0 Depends: R(>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer Imports: parallel, matrixStats, foreach, Matrix, gplots, graphics, grDevices, stats, utils, Wrench Suggests: annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay, IHW License: Artistic-2.0 Package: metahdep Version: 1.62.0 Depends: R (>= 2.10), methods Suggests: affyPLM License: GPL-3 Archs: x64 Package: metaMS Version: 1.40.0 Depends: R (>= 4.0), methods, CAMERA, xcms (>= 1.35) Imports: Matrix, tools, robustbase, BiocGenerics, graphics, stats, utils Suggests: metaMSdata, RUnit License: GPL (>= 2) Package: MetaNeighbor Version: 1.24.0 Depends: R(>= 3.5) Imports: grDevices, graphics, methods, stats (>= 3.4), utils (>= 3.4), Matrix (>= 1.2), matrixStats (>= 0.54), beanplot (>= 1.2), gplots (>= 3.0.1), RColorBrewer (>= 1.1.2), SummarizedExperiment (>= 1.12), SingleCellExperiment, igraph, dplyr, tidyr, tibble, ggplot2 Suggests: knitr (>= 1.17), rmarkdown (>= 1.6), testthat (>= 1.0.2), UpSetR License: MIT + file LICENSE Package: MetaPhOR Version: 1.6.0 Depends: R (>= 4.2.0) Imports: utils, ggplot2, ggrepel, stringr, pheatmap, grDevices, stats, clusterProfiler, RecordLinkage, RCy3 Suggests: BiocStyle, knitr, rmarkdown, kableExtra License: Artistic-2.0 Package: metapod Version: 1.12.0 Imports: Rcpp LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown License: GPL-3 Archs: x64 Package: metapone Version: 1.10.0 Depends: R (>= 4.1.0), BiocParallel, fields, markdown, fdrtool, fgsea, ggplot2, ggrepel Imports: methods Suggests: rmarkdown, knitr License: Artistic-2.0 Package: metaSeq Version: 1.44.0 Depends: R (>= 2.13.0), NOISeq, snow, Rcpp License: Artistic-2.0 Package: metaseqR2 Version: 1.16.0 Depends: R (>= 4.0.0), DESeq2, limma, locfit, splines Imports: ABSSeq, Biobase, BiocGenerics, BiocParallel, biomaRt, Biostrings, corrplot, DSS, DT, EDASeq, edgeR, genefilter, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, gplots, graphics, grDevices, harmonicmeanp, heatmaply, htmltools, httr, IRanges, jsonlite, lattice, log4r, magrittr, MASS, Matrix, methods, NBPSeq, pander, parallel, qvalue, rmarkdown, rmdformats, Rsamtools, RSQLite, rtracklayer, S4Vectors, stats, stringr, SummarizedExperiment, survcomp, txdbmaker, utils, VennDiagram, vsn, yaml, zoo Suggests: BiocStyle, BiocManager, BSgenome, knitr, RMySQL, RUnit Enhances: TCC License: GPL (>= 3) Archs: x64 Package: MetaVolcanoR Version: 1.18.0 Depends: R (>= 4.1.1) Imports: methods, data.table, dplyr, tidyr, plotly, ggplot2, cowplot, parallel, metafor, metap, rlang, topconfects, grDevices, graphics, stats, htmlwidgets Suggests: knitr, markdown, rmarkdown, testthat License: GPL-3 Package: MetCirc Version: 1.34.0 Depends: R (>= 3.5), amap (>= 0.8), circlize (>= 0.3.9), scales (>= 0.3.0), shiny (>= 1.0.0), Spectra (>= 1.4.3) Imports: ggplot2 (>= 3.2.1), MsCoreUtils (>= 1.9.2), S4Vectors (>= 0.22.0) Suggests: BiocGenerics, graphics (>= 3.5), grDevices (>= 3.5), knitr (>= 1.11), testthat (>= 2.2.1) License: GPL (>= 3) Package: methimpute Version: 1.26.0 Depends: R (>= 3.5.0), GenomicRanges, ggplot2 Imports: Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats, GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm, data.table LinkingTo: Rcpp Suggests: knitr, BiocStyle License: Artistic-2.0 Archs: x64 Package: methInheritSim Version: 1.26.0 Depends: R (>= 3.5.0) Imports: methylKit, GenomicRanges, GenomeInfoDb, parallel, BiocGenerics, S4Vectors, methods, stats, IRanges, msm Suggests: BiocStyle, knitr, rmarkdown, RUnit, methylInheritance License: Artistic-2.0 Package: MethPed Version: 1.32.0 Depends: R (>= 3.0.0), Biobase Imports: randomForest, grDevices, graphics, stats Suggests: BiocStyle, knitr, markdown, impute License: GPL-2 Package: MethReg Version: 1.14.0 Depends: R (>= 4.0) Imports: dplyr, plyr, GenomicRanges, SummarizedExperiment, DelayedArray, ggplot2, ggpubr, tibble, tidyr, S4Vectors, sesameData, sesame, AnnotationHub, ExperimentHub, stringr, readr, methods, stats, Matrix, MASS, rlang, pscl, IRanges, sfsmisc, progress, utils, openxlsx, JASPAR2024, RSQLite, TFBSTools Suggests: rmarkdown, BiocStyle, testthat (>= 2.1.0), parallel, R.utils, doParallel, reshape2, motifmatchr, matrixStats, biomaRt, dorothea, viper, stageR, BiocFileCache, png, htmltools, knitr, jpeg, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, data.table, downloader License: GPL-3 Package: methrix Version: 1.18.0 Depends: R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment Imports: rtracklayer, DelayedArray, HDF5Array, BSgenome, DelayedMatrixStats, parallel, methods, ggplot2, S4Vectors, matrixStats, graphics, stats, utils, GenomicRanges, IRanges Suggests: knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, BSgenome.Hsapiens.UCSC.hg19, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) License: MIT + file LICENSE Package: MethTargetedNGS Version: 1.36.0 Depends: R (>= 3.1.2), stringr, seqinr, gplots, Biostrings, pwalign Imports: utils, graphics, stats License: Artistic-2.0 Package: MethylAid Version: 1.38.0 Depends: R (>= 3.4) Imports: Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0), methods, RColorBrewer, shiny, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit License: GPL (>= 2) Package: methylCC Version: 1.18.0 Depends: R (>= 3.6), FlowSorted.Blood.450k Imports: Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr, minfi, bsseq, quadprog, plyranges, stats, utils, bumphunter, genefilter, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 Suggests: rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 License: GPL-3 Package: methylclock Version: 1.10.0 Depends: R (>= 4.1.0), methylclockData, devtools, quadprog Imports: Rcpp (>= 1.0.6), ExperimentHub, dplyr, impute, PerformanceAnalytics, Biobase, ggpmisc, tidyverse, ggplot2, ggpubr, minfi, tibble, RPMM, stats, graphics, tidyr, gridExtra, preprocessCore, dynamicTreeCut, planet LinkingTo: Rcpp Suggests: BiocStyle, knitr, GEOquery, rmarkdown License: MIT + file LICENSE Archs: x64 Package: methylGSA Version: 1.22.0 Depends: R (>= 3.5) Imports: RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler, missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db, AnnotationDbi, shiny, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr, rmarkdown, testthat, enrichplot License: GPL-2 Package: methyLImp2 Version: 1.0.0 Depends: R (>= 4.3.0), ChAMPdata Imports: BiocParallel, parallel, stats, methods, corpcor, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, spelling, testthat (>= 3.0.0) License: GPL-3 Package: methylInheritance Version: 1.28.0 Depends: R (>= 3.5) Imports: methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors, methods, parallel, ggplot2, gridExtra, rebus Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim License: Artistic-2.0 Package: methylKit Version: 1.30.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.18.1), methods Imports: IRanges, data.table (>= 1.9.6), parallel, S4Vectors (>= 0.13.13), GenomeInfoDb, KernSmooth, qvalue, emdbook, Rsamtools, gtools, fastseg, rtracklayer, mclust, mgcv, Rcpp, R.utils, limma, grDevices, graphics, stats, utils LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager License: Artistic-2.0 Archs: x64 Package: MethylMix Version: 2.34.0 Depends: R (>= 3.2.0) Imports: foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute, data.table, limma, R.matlab, digest Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown License: GPL-2 Package: methylMnM Version: 1.42.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 Archs: x64 Package: methylPipe Version: 1.38.0 Depends: R (>= 3.5.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools Imports: marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, GenomeInfoDb, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR License: GPL (>= 2) Archs: x64 Package: methylscaper Version: 1.12.0 Depends: R (>= 4.1.0) Imports: shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings, pwalign, Rfast, grDevices, graphics, stats, utils, tools, methods, shinyFiles, data.table, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, devtools, R.utils License: GPL-2 Package: MethylSeekR Version: 1.44.0 Depends: rtracklayer (>= 1.16.3), parallel (>= 2.15.1), mhsmm (>= 0.4.4) Imports: IRanges (>= 1.16.3), BSgenome (>= 1.26.1), GenomicRanges (>= 1.10.5), geneplotter (>= 1.34.0), graphics (>= 2.15.2), grDevices (>= 2.15.2), parallel (>= 2.15.2), stats (>= 2.15.2), utils (>= 2.15.2) Suggests: BSgenome.Hsapiens.UCSC.hg18 License: GPL (>= 2) Package: methylSig Version: 1.16.0 Depends: R (>= 3.6) Imports: bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, GenomeInfoDb, GenomicRanges, methods, parallel, stats, S4Vectors Suggests: BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr License: GPL-3 Package: methylumi Version: 2.50.0 Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi Imports: BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, illuminaio, GenomicFeatures Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr License: GPL-2 Package: MetID Version: 1.22.0 Depends: R (>= 3.5) Imports: utils (>= 3.3.1), stats (>= 3.4.2), devtools (>= 1.13.0), stringr (>= 1.3.0), Matrix (>= 1.2-12), igraph (>= 1.2.1), ChemmineR (>= 2.30.2) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8) License: Artistic-2.0 Package: MetNet Version: 1.22.0 Depends: R (>= 4.0), S4Vectors (>= 0.28.1), SummarizedExperiment (>= 1.20.0) Imports: bnlearn (>= 4.3), BiocParallel (>= 1.12.0), corpcor (>= 1.6.10), dplyr (>= 1.0.3), ggplot2 (>= 3.3.3), GeneNet (>= 1.2.15), GENIE3 (>= 1.7.0), methods (>= 3.5), parmigene (>= 1.0.2), psych (>= 2.1.6), rlang (>= 0.4.10), stabs (>= 0.6), stats (>= 3.6), tibble (>= 3.0.5), tidyr (>= 1.1.2) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), glmnet (>= 4.1-1), igraph (>= 1.1.2), knitr (>= 1.11), rmarkdown (>= 1.15), testthat (>= 2.2.1), Spectra (>= 1.4.1), MsCoreUtils (>= 1.6.0) License: GPL (>= 3) Package: mfa Version: 1.26.0 Depends: R (>= 3.4.0) Imports: methods, stats, ggplot2, Rcpp, dplyr, ggmcmc, MCMCpack, MCMCglmm, coda, magrittr, tibble, Biobase LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) Archs: x64 Package: Mfuzz Version: 2.64.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 Package: MGFM Version: 1.38.0 Depends: AnnotationDbi,annotate Suggests: hgu133a.db License: GPL-3 Package: MGFR Version: 1.30.0 Depends: R (>= 3.5) Imports: biomaRt, annotate License: GPL-3 Package: MGnifyR Version: 1.0.0 Depends: R(>= 4.4.0), MultiAssayExperiment, TreeSummarizedExperiment, SummarizedExperiment, BiocGenerics Imports: mia, ape, dplyr, httr, methods, plyr, reshape2, S4Vectors, urltools, utils, tidyjson Suggests: biomformat, broom, ggplot2, knitr, rmarkdown, testthat, xml2, BiocStyle, miaViz, vegan, scater, phyloseq, magick License: Artistic-2.0 | file LICENSE Package: mgsa Version: 1.52.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 Archs: x64 Package: mia Version: 1.12.0 Depends: R (>= 4.0), SummarizedExperiment, SingleCellExperiment, TreeSummarizedExperiment (>= 1.99.3), MultiAssayExperiment Imports: methods, stats, utils, MASS, ape, decontam, vegan, BiocGenerics, S4Vectors, IRanges, Biostrings, DECIPHER, BiocParallel, DelayedArray, DelayedMatrixStats, scuttle, scater, DirichletMultinomial, rlang, dplyr, tibble, tidyr, bluster, MatrixGenerics Suggests: testthat, knitr, patchwork, BiocStyle, yaml, phyloseq, dada2, stringr, biomformat, reldist, ade4, microbiomeDataSets, rmarkdown License: Artistic-2.0 | file LICENSE Package: miaSim Version: 1.10.0 Depends: TreeSummarizedExperiment Imports: SummarizedExperiment, deSolve, stats, poweRlaw, MatrixGenerics, S4Vectors Suggests: ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy License: Artistic-2.0 | file LICENSE Package: miaViz Version: 1.12.0 Depends: R (>= 4.0), SummarizedExperiment, TreeSummarizedExperiment, mia (>= 0.99), ggplot2, ggraph (>= 2.0) Imports: methods, stats, S4Vectors, BiocGenerics, BiocParallel, DelayedArray, scater, ggtree, ggnewscale, viridis, tibble, tidytree, tidygraph, rlang, purrr, tidyr, dplyr, ape, DirichletMultinomial, ggrepel, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat, patchwork, vegan, microbiomeDataSets, bluster License: Artistic-2.0 | file LICENSE Package: MiChip Version: 1.58.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) Package: microbiome Version: 1.26.0 Depends: R (>= 3.6.0), phyloseq, ggplot2 Imports: Biostrings, compositions, dplyr, reshape2, Rtsne, scales, stats, tibble, tidyr, utils, vegan Suggests: BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat License: BSD_2_clause + file LICENSE Package: microbiomeDASim Version: 1.18.0 Depends: R (>= 3.6.0) Imports: graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply, stats, phyloseq, metagenomeSeq, Biobase Suggests: testthat (>= 2.1.0), knitr, devtools License: MIT + file LICENSE Package: microbiomeExplorer Version: 1.14.0 Depends: shiny, magrittr, metagenomeSeq, Biobase Imports: shinyjs (>= 2.0.0), shinydashboard, shinycssloaders, shinyWidgets, rmarkdown (>= 1.9.0), DESeq2, RColorBrewer, dplyr, tidyr, purrr, rlang, knitr, readr, DT (>= 0.12.0), biomformat, tools, stringr, vegan, matrixStats, heatmaply, car, broom, limma, reshape2, tibble, forcats, lubridate, methods, plotly (>= 4.9.1) Suggests: V8, testthat (>= 2.1.0) License: MIT + file LICENSE Package: microbiomeMarker Version: 1.10.0 Depends: R (>= 4.1.0) Imports: dplyr, phyloseq, magrittr, purrr, MASS, utils, ggplot2, tibble, rlang, stats, coin, ggtree, tidytree, methods, IRanges, tidyr, patchwork, ggsignif, metagenomeSeq, DESeq2, edgeR, BiocGenerics, Biostrings, yaml, biomformat, S4Vectors, Biobase, ComplexHeatmap, ANCOMBC, caret, limma, ALDEx2, multtest, plotROC, vegan, pROC, BiocParallel Suggests: testthat, covr, glmnet, Matrix, kernlab, e1071, ranger, knitr, rmarkdown, BiocStyle, withr License: GPL-3 Package: MicrobiomeProfiler Version: 1.10.0 Depends: R (>= 4.2.0) Imports: clusterProfiler (>= 4.5.2), config, DT, enrichplot, golem, gson, methods, magrittr, shiny (>= 1.6.0), shinyWidgets, shinycustomloader, htmltools, ggplot2, graphics, stats, utils Suggests: rmarkdown, knitr, testthat (>= 3.0.0), prettydoc License: GPL-2 Package: MicrobiotaProcess Version: 1.16.0 Depends: R (>= 4.0.0) Imports: ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel, vegan, zoo, ggtree, tidytree (>= 0.4.2), MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, patchwork, ggstar, tidyselect, SummarizedExperiment, foreach, treeio (>= 1.17.2), pillar, cli, plyr, dtplyr, ggtreeExtra, data.table, ggfun (>= 0.1.1) Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, ggupset, ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial, ggpp, BiocManager License: GPL (>= 3.0) Package: microRNA Version: 1.62.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) License: Artistic-2.0 Archs: x64 Package: MICSQTL Version: 1.2.2 Depends: R (>= 4.3.0), SummarizedExperiment, stats Imports: TCA, nnls, purrr, TOAST, magrittr, BiocParallel, ggplot2, ggpubr, ggridges, glue, S4Vectors, dirmult Suggests: testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle License: GPL-3 Package: midasHLA Version: 1.12.0 Depends: R (>= 4.1), MultiAssayExperiment (>= 1.8.3) Imports: assertthat (>= 0.2.0), broom (>= 0.5.1), dplyr (>= 0.8.0.1), formattable (>= 0.2.0.1), HardyWeinberg (>= 1.6.3), kableExtra (>= 1.1.0), knitr (>= 1.21), magrittr (>= 1.5), methods, stringi (>= 1.2.4), rlang (>= 0.3.1), S4Vectors (>= 0.20.1), stats, SummarizedExperiment (>= 1.12.0), tibble (>= 2.0.1), utils, qdapTools (>= 1.3.3) Suggests: broom.mixed (>= 0.2.4), cowplot (>= 1.0.0), devtools (>= 2.0.1), ggplot2 (>= 3.1.0), ggpubr (>= 0.2.5), rmarkdown, seqinr (>= 3.4-5), survival (>= 2.43-3), testthat (>= 2.0.1), tidyr (>= 1.1.2) License: MIT + file LICENCE Package: miloR Version: 2.0.0 Depends: R (>= 4.0.0), edgeR Imports: BiocNeighbors, BiocGenerics, SingleCellExperiment, Matrix (>= 1.3-0), MatrixGenerics, S4Vectors, stats, stringr, methods, igraph, irlba, utils, cowplot, BiocParallel, BiocSingular, limma, ggplot2, tibble, matrixStats, ggraph, gtools, SummarizedExperiment, patchwork, tidyr, dplyr, ggrepel, ggbeeswarm, RColorBrewer, grDevices, Rcpp, numDeriv LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData, MouseThymusAgeing, magick, RCurl, MASS, curl, scRNAseq, graphics License: GPL-3 + file LICENSE Archs: x64 Package: mimager Version: 1.28.0 Depends: Biobase Imports: BiocGenerics, S4Vectors, preprocessCore, grDevices, methods, grid, gtable, scales, DBI, affy, affyPLM, oligo, oligoClasses Suggests: knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind, affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1 License: MIT + file LICENSE Package: mina Version: 1.12.0 Depends: R (>= 4.0.0) Imports: methods, stats, Rcpp, MCL, RSpectra, apcluster, bigmemory, foreach, ggplot2, parallel, parallelDist, reshape2, plyr, biganalytics, stringr, Hmisc, utils LinkingTo: Rcpp, RcppParallel, RcppArmadillo Suggests: knitr, rmarkdown Enhances: doMC License: GPL Archs: x64 Package: MineICA Version: 1.44.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr, ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster, marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate, Hmisc, fastICA, JADE Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX, future, future.apply Enhances: doMC License: GPL-2 Package: minet Version: 3.62.0 Imports: infotheo License: Artistic-2.0 Archs: x64 Package: minfi Version: 1.50.0 Depends: methods, BiocGenerics (>= 0.15.3), GenomicRanges, SummarizedExperiment (>= 1.1.6), Biostrings, bumphunter (>= 1.1.9) Imports: S4Vectors, GenomeInfoDb, Biobase (>= 2.33.2), IRanges, beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma, preprocessCore, illuminaio (>= 0.23.2), DelayedMatrixStats (>= 1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog, data.table, GEOquery, stats, grDevices, graphics, utils, DelayedArray (>= 0.15.16), HDF5Array, BiocParallel Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools License: Artistic-2.0 Package: MinimumDistance Version: 1.48.0 Depends: R (>= 3.5.0), VanillaICE (>= 1.47.1) Imports: methods, BiocGenerics, MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges, GenomeInfoDb, GenomicRanges (>= 1.17.16), SummarizedExperiment (>= 1.15.4), oligoClasses, DNAcopy, ff, foreach, matrixStats, lattice, data.table, grid, stats, utils Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit Enhances: snow, doSNOW License: Artistic-2.0 Package: MiPP Version: 1.76.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) Package: miQC Version: 1.12.0 Depends: R (>= 3.5.0) Imports: SingleCellExperiment, flexmix, ggplot2, splines Suggests: scRNAseq, scater, BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE Package: MIRA Version: 1.26.0 Depends: R (>= 3.5) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 Package: MiRaGE Version: 1.46.0 Depends: R (>= 3.1.0), Biobase(>= 2.23.3) Imports: BiocGenerics, S4Vectors, AnnotationDbi, BiocManager Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData License: GPL Package: miRBaseConverter Version: 1.28.0 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils, rmarkdown License: GPL (>= 2) Package: miRcomp Version: 1.34.0 Depends: R (>= 3.2), Biobase (>= 2.22.0), miRcompData Imports: utils, methods, graphics, KernSmooth, stats Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny License: GPL-3 | file LICENSE Package: mirIntegrator Version: 1.34.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) Package: miRLAB Version: 1.34.0 Imports: methods, stats, utils, RCurl, httr, stringr, Hmisc, energy, entropy, gplots, glmnet, impute, limma, pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc, InvariantCausalPrediction, Category, GOstats, org.Hs.eg.db Suggests: knitr,BiocGenerics, AnnotationDbi,RUnit,rmarkdown License: GPL (>= 2) Package: miRmine Version: 1.26.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, DESeq2 License: GPL (>= 3) Package: miRNAmeConverter Version: 1.32.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi, reshape2 Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 Package: miRNApath Version: 1.64.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 Package: miRNAtap Version: 1.38.0 Depends: R (>= 3.3.0), AnnotationDbi Imports: DBI, RSQLite, stringr, sqldf, plyr, methods Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat License: GPL-2 Package: miRSM Version: 2.0.0 Depends: R (>= 3.5.0) Imports: WGCNA, flashClust, dynamicTreeCut, GFA, igraph, linkcomm, MCL, fabia, NMF, biclust, iBBiG, BicARE, isa2, s4vd, BiBitR, rqubic, Biobase, PMA, stats, dbscan, subspace, mclust, SOMbrero, ppclust, Rcpp, utils, SummarizedExperiment, GSEABase, org.Hs.eg.db, clusterProfiler, ReactomePA, DOSE, MatrixCorrelation, energy Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 Archs: x64 Package: miRspongeR Version: 2.8.0 Depends: R (>= 3.5.0) Imports: corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, linkcomm, utils, Rcpp, org.Hs.eg.db, foreach, doParallel Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 Archs: x64 Package: mirTarRnaSeq Version: 1.12.0 Depends: R (>= 4.1.0), ggplot2 Imports: purrr, MASS, pscl, assertthat, caTools, dplyr, pheatmap, reshape2, corrplot, grDevices, graphics, stats, utils, data.table, R.utils, viridis Suggests: BiocStyle, knitr, rmarkdown, R.cache, SPONGE License: MIT + file LICENSE Package: missMethyl Version: 1.38.0 Depends: R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Imports: AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IRanges, limma, methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod, stringr, SummarizedExperiment Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub License: GPL-2 Package: missRows Version: 1.24.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, stats, gtools, S4Vectors Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 Package: mistyR Version: 1.12.0 Depends: R (>= 4.0) Imports: assertthat, caret, deldir, digest, distances, dplyr (>= 1.1.0), filelock, furrr (>= 0.2.0), ggplot2, methods, purrr, ranger, readr (>= 2.0.0), ridge, rlang, rlist, R.utils, stats, stringr, tibble, tidyr, tidyselect (>= 1.2.0), utils, withr Suggests: BiocStyle, covr, earth, future, igraph (>= 1.2.7), iml, kernlab, knitr, MASS, rmarkdown, RSNNS, testthat (>= 3.0.0), xgboost License: GPL-3 Package: mitch Version: 1.16.0 Depends: R (>= 4.3) Imports: stats, grDevices, graphics, utils, MASS, plyr, reshape2, parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2, gplots, beeswarm, echarts4r, kableExtra Suggests: stringi, testthat (>= 2.1.0), HGNChelper, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: CC BY-SA 4.0 + file LICENSE Package: mitoClone2 Version: 1.10.0 Depends: R (>= 4.1.0) Imports: reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2 LinkingTo: Rhtslib (>= 1.13.1) Suggests: knitr, rmarkdown, Biostrings, testthat License: GPL-3 Archs: x64 Package: mixOmics Version: 6.28.0 Depends: R (>= 3.5.0), MASS, lattice, ggplot2 Imports: igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, ggrepel, BiocParallel, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, rgl License: GPL (>= 2) Package: MLInterfaces Version: 1.84.0 Depends: R (>= 3.5), Rcpp, methods, BiocGenerics (>= 0.13.11), Biobase, annotate, cluster Imports: gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis, shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench, stats4, tools, grDevices, graphics, stats, magrittr, SummarizedExperiment Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party, klaR, BiocStyle, knitr, testthat Enhances: parallel License: LGPL Package: MLP Version: 1.52.0 Imports: AnnotationDbi, gplots, graphics, stats, utils Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, org.Mmu.eg.db, KEGGREST, annotate, Rgraphviz, GOstats, graph, limma, mouse4302.db, reactome.db License: GPL-3 Package: MLSeq Version: 2.22.0 Depends: caret, ggplot2 Imports: testthat, VennDiagram, pamr, methods, DESeq2, edgeR, limma, Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq, xtable Suggests: knitr, e1071, kernlab License: GPL (>= 2) Package: MMDiff2 Version: 1.32.0 Depends: R (>= 3.5.0), Rsamtools, Biobase Imports: GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2, RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 License: Artistic-2.0 Package: MMUPHin Version: 1.18.1 Depends: R (>= 3.6) Imports: Maaslin2, metafor, fpc, igraph, ggplot2, dplyr, tidyr, stringr, cowplot, utils, stats, grDevices Suggests: testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter License: MIT + file LICENSE Package: mnem Version: 1.20.0 Depends: R (>= 4.1) Imports: cluster, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices, e1071, ggplot2, wesanderson LinkingTo: Rcpp, RcppEigen Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM, BiocStyle License: GPL-3 Archs: x64 Package: moanin Version: 1.12.0 Depends: R (>= 4.0), SummarizedExperiment, topGO, stats Imports: S4Vectors, MASS (>= 1.0.0), limma, viridis, edgeR, graphics, methods, grDevices, reshape2, NMI, zoo, ClusterR, splines, matrixStats Suggests: testthat (>= 1.0.0), timecoursedata, knitr, rmarkdown, markdown, covr, BiocStyle License: BSD 3-clause License + file LICENSE Package: mobileRNA Version: 1.0.11 Depends: R (>= 4.3.0) Imports: dplyr, tidyr, ggplot2, BiocGenerics, DESeq2, edgeR, ggrepel, grDevices, pheatmap, utils, tidyselect, progress, RColorBrewer, GenomicRanges, rtracklayer, data.table, SimDesign, scales, IRanges, stats, methods, Biostrings, reticulate, S4Vectors, GenomeInfoDb, SummarizedExperiment, rlang, bioseq, grid Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE Package: MODA Version: 1.30.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) Package: ModCon Version: 1.12.0 Depends: data.table, parallel, utils, stats, R (>= 4.1) Suggests: testthat, knitr, rmarkdown, dplyr, shinycssloaders, shiny, shinyFiles, shinydashboard, shinyjs License: GPL-3 + file LICENSE Package: Modstrings Version: 1.20.0 Depends: R (>= 3.6), Biostrings (>= 2.51.5) Imports: methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges, XVector, stringi, stringr, crayon, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 Package: MOFA2 Version: 1.14.0 Depends: R (>= 4.0) Imports: rhdf5, dplyr, tidyr, reshape2, pheatmap, ggplot2, methods, RColorBrewer, cowplot, ggrepel, reticulate, HDF5Array, grDevices, stats, magrittr, forcats, utils, corrplot, DelayedArray, Rtsne, uwot, basilisk, stringi Suggests: knitr, testthat, Seurat, SeuratObject, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown, data.table, tidyverse, BiocStyle, Matrix, markdown License: file LICENSE Package: MOGAMUN Version: 1.14.0 Imports: stats, utils, RCy3, stringr, graphics, grDevices, RUnit, BiocParallel, igraph Suggests: knitr, markdown License: GPL-3 + file LICENSE Package: mogsa Version: 1.38.0 Depends: R (>= 3.4.0) Imports: methods, graphite, genefilter, BiocGenerics, gplots, GSEABase, Biobase, parallel, corpcor, svd, cluster, grDevices, graphics, stats, utils Suggests: BiocStyle, knitr, org.Hs.eg.db License: GPL-2 Package: MoleculeExperiment Version: 1.4.1 Depends: R (>= 2.10) Imports: SpatialExperiment, Matrix, purrr, data.table, dplyr (>= 1.1.1), magrittr, rjson, utils, methods, terra, ggplot2, rlang, cli, EBImage, rhdf5, BiocParallel, S4Vectors, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE Package: MOMA Version: 1.16.0 Depends: R (>= 4.0) Imports: circlize, cluster, ComplexHeatmap, dplyr, ggplot2, graphics, grid, grDevices, magrittr, methods, MKmisc, MultiAssayExperiment, parallel, qvalue, RColorBrewer, readr, reshape2, rlang, stats, stringr, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, viper License: GPL-3 Package: monaLisa Version: 1.10.0 Depends: R (>= 4.1) Imports: methods, stats, utils, grDevices, graphics, BiocGenerics, GenomicRanges, TFBSTools, Biostrings, IRanges, stabs, BSgenome, glmnet, S4Vectors, SummarizedExperiment, BiocParallel, grid, circlize, ComplexHeatmap (>= 2.11.1), XVector, GenomeInfoDb, tools, vioplot, RSQLite Suggests: JASPAR2020, JASPAR2024, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, testthat, BiocStyle, gridExtra License: GPL (>= 3) Package: monocle Version: 2.32.0 Depends: R (>= 2.10.0), methods, Matrix (>= 1.2-6), Biobase, ggplot2 (>= 1.0.0), VGAM (>= 1.0-6), DDRTree (>= 0.1.4), Imports: parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>= 0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>= 2.0.0), matrixStats, Rtsne, MASS, reshape2, leidenbase (>= 0.1.9), limma, tibble, dplyr, pheatmap, stringr, proxy, slam, viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>= 0.12.0) LinkingTo: Rcpp Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat License: Artistic-2.0 Archs: x64 Package: Moonlight2R Version: 1.2.0 Depends: R (>= 4.3), doParallel, foreach Imports: parmigene, randomForest, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, grDevices, graphics, GEOquery, stats, purrr, RISmed, grid, utils, ComplexHeatmap, GenomicRanges, dplyr, fuzzyjoin, rtracklayer, magrittr, qpdf, readr, seqminer, stringr, tibble, tidyHeatmap, tidyr, AnnotationHub, easyPubMed, org.Hs.eg.db, EpiMix, BiocGenerics, ggplot2, ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), devtools, roxygen2, png License: GPL-3 Package: MoonlightR Version: 1.30.0 Depends: R (>= 3.5), doParallel, foreach Imports: parmigene, randomForest, SummarizedExperiment, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats, RISmed, grid, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png, edgeR License: GPL (>= 3) Package: mosaics Version: 2.42.0 Depends: R (>= 3.0.0), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, S4Vectors LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) Archs: x64 Package: mosbi Version: 1.10.0 Depends: R (>= 4.1) Imports: Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust, isa2, QUBIC, akmbiclust, RColorBrewer LinkingTo: Rcpp, BH, RcppParallel Suggests: knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE Archs: x64 Package: mosdef Version: 1.0.0 Depends: R (>= 4.4.0) Imports: DT, ggplot2, ggforce, ggrepel, htmltools, methods, AnnotationDbi, topGO, GO.db, clusterProfiler, goseq, utils, RColorBrewer, rlang, DESeq2, scales, SummarizedExperiment, S4Vectors, stats Suggests: knitr, rmarkdown, macrophage, org.Hs.eg.db, GeneTonic, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg38.knownGene, BiocStyle License: MIT + file LICENSE Package: MOSim Version: 2.0.0 Depends: R (>= 4.2.0) Imports: HiddenMarkov, zoo, IRanges, S4Vectors, dplyr, ggplot2, lazyeval, matrixStats, methods, rlang, stringi, stringr, scran, Seurat, Signac, edgeR, Rcpp LinkingTo: cpp11, Rcpp Suggests: testthat, knitr, rmarkdown, codetools, BiocStyle, stats, utils, purrr, scales, tibble, tidyr, Biobase, scater, SingleCellExperiment, decor, markdown, Rsamtools, igraph, leiden, bluster License: GPL-3 Archs: x64 Package: Motif2Site Version: 1.8.0 Depends: R (>= 4.1) Imports: S4Vectors, stats, utils, methods, grDevices, graphics, BiocGenerics, BSgenome, GenomeInfoDb, MASS, IRanges, GenomicRanges, Biostrings, GenomicAlignments, edgeR, mixtools Suggests: BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805 License: GPL-2 Package: motifbreakR Version: 2.18.0 Depends: R (>= 4.3.0), grid, MotifDb Imports: methods, grDevices, stringr, parallel, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, Biostrings, BSgenome, rtracklayer, VariantAnnotation, BiocParallel, motifStack, Gviz, matrixStats, TFMPvalue, SummarizedExperiment, pwalign Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP155.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle License: GPL-2 Package: motifcounter Version: 1.28.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 Archs: x64 Package: MotifDb Version: 1.46.0 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings Imports: rtracklayer, splitstackshape Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR, markdown License: Artistic-2.0 | file LICENSE License_is_FOSS: no License_restricts_use: yes Package: motifmatchr Version: 1.26.0 Depends: R (>= 3.3) Imports: Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, GenomeInfoDb LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 + file LICENSE Archs: x64 Package: motifStack Version: 1.48.0 Depends: R (>= 2.15.1), methods, grid Imports: ade4, Biostrings, ggplot2, grDevices, graphics, htmlwidgets, stats, stats4, utils, XML, TFBSTools Suggests: Cairo, grImport, grImport2, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr, RUnit, rmarkdown, JASPAR2020 License: GPL (>= 2) Package: motifTestR Version: 1.0.3 Depends: Biostrings, GenomicRanges, ggplot2 (>= 3.5.0), R (>= 4.3.0), Imports: GenomeInfoDb, harmonicmeanp, IRanges, matrixStats, methods, parallel, patchwork, rlang, S4Vectors, stats, universalmotif Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, extraChIPs, ggdendro, knitr, MotifDb, rmarkdown, rtracklayer, testthat (>= 3.0.0) License: GPL-3 Package: MouseFM Version: 1.14.0 Depends: R (>= 4.0.0) Imports: httr, curl, GenomicRanges, dplyr, ggplot2, reshape2, scales, gtools, tidyr, data.table, jsonlite, rlist, GenomeInfoDb, methods, biomaRt, stats, IRanges Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 Package: MPFE Version: 1.40.0 License: GPL (>= 3) Package: mpra Version: 1.26.0 Depends: R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment, limma Imports: S4Vectors, scales, stats, graphics, statmod Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 Package: MPRAnalyze Version: 1.22.0 Imports: BiocParallel, methods, progress, stats, SummarizedExperiment Suggests: knitr License: GPL-3 Package: msa Version: 1.36.0 Depends: R (>= 3.3.0), methods, Biostrings (>= 2.40.0) Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors, tools LinkingTo: Rcpp Suggests: Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign License: GPL (>= 2) Archs: x64 Package: MSA2dist Version: 1.8.0 Depends: R (>= 4.4.0) Imports: Rcpp, Biostrings, GenomicRanges, IRanges, ape, doParallel, dplyr, foreach, methods, parallel, pwalign, rlang, seqinr, stats, stringi, stringr, tibble, tidyr, utils LinkingTo: Rcpp, RcppThread Suggests: rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle License: GPL-3 + file LICENSE Archs: x64 Package: MsBackendMassbank Version: 1.12.0 Depends: R (>= 4.0), Spectra (>= 1.9.12) Imports: BiocParallel, S4Vectors, IRanges, methods, ProtGenerics (>= 1.35.3), MsCoreUtils, DBI, utils Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, rmarkdown License: Artistic-2.0 Package: MsBackendMgf Version: 1.12.0 Depends: R (>= 4.0), Spectra (>= 1.5.14) Imports: ProtGenerics (>= 1.35.3), BiocParallel, S4Vectors, IRanges, MsCoreUtils, methods, stats Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown License: Artistic-2.0 Package: MsBackendMsp Version: 1.8.0 Depends: R (>= 4.1.0), Spectra (>= 1.5.14) Imports: ProtGenerics (>= 1.35.3), BiocParallel, S4Vectors, IRanges, MsCoreUtils, methods, stats Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown License: Artistic-2.0 Package: MsBackendRawFileReader Version: 1.10.0 Depends: R (>= 4.1), methods, Spectra (>= 1.5.8) Imports: ProtGenerics (>= 1.35.3), MsCoreUtils, S4Vectors, IRanges, rawrr (>= 1.10.1), utils, BiocParallel Suggests: BiocStyle (>= 2.5), ExperimentHub, MsBackendMgf, knitr, lattice, mzR, protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat License: GPL-3 Package: MsBackendSql Version: 1.4.0 Depends: R (>= 4.2.0), Spectra (>= 1.9.12) Imports: BiocParallel, S4Vectors, methods, ProtGenerics (>= 1.35.3), DBI, MsCoreUtils, IRanges, data.table, progress, BiocGenerics Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, msdata, rmarkdown, microbenchmark, mzR License: Artistic-2.0 Package: MsCoreUtils Version: 1.16.0 Depends: R (>= 3.6.0) Imports: methods, S4Vectors, MASS, stats, clue LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD, impute, norm, pcaMethods, vsn, Matrix, preprocessCore, missForest Enhances: HDF5Array License: Artistic-2.0 Archs: x64 Package: MsDataHub Version: 1.4.0 Imports: ExperimentHub, utils Suggests: ExperimentHubData, DT, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), Spectra, mzR, PSMatch, QFeatures (>= 1.13.3) License: Artistic-2.0 Package: MsExperiment Version: 1.6.0 Depends: R (>= 4.2), ProtGenerics (>= 1.35.2), Imports: methods, S4Vectors, IRanges, Spectra, SummarizedExperiment, QFeatures, DBI, BiocGenerics Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown, rpx, mzR, msdata, MsBackendSql (>= 1.3.2), RSQLite License: Artistic-2.0 Package: MsFeatures Version: 1.12.0 Depends: R (>= 4.1) Imports: methods, ProtGenerics (>= 1.23.5), MsCoreUtils, SummarizedExperiment, stats Suggests: testthat, roxygen2, BiocStyle, pheatmap, knitr, rmarkdown License: Artistic-2.0 Package: msgbsR Version: 1.28.0 Depends: R (>= 3.5.0), GenomicRanges, methods Imports: BSgenome, easyRNASeq, edgeR, GenomicAlignments, GenomicFeatures, GenomeInfoDb, ggbio, ggplot2, IRanges, parallel, plyr, Rsamtools, R.utils, stats, SummarizedExperiment, S4Vectors, utils Suggests: roxygen2, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-2 Package: msImpute Version: 1.14.0 Depends: R (>= 3.5.0) Imports: softImpute, methods, stats, graphics, pdist, reticulate, scran, data.table, FNN, matrixStats, limma, mvtnorm, tidyr, dplyr Suggests: BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD License: GPL (>= 2) Package: mslp Version: 1.6.0 Depends: R (>= 4.2.0) Imports: data.table (>= 1.13.0), doRNG, fmsb, foreach, magrittr, org.Hs.eg.db, pROC, randomForest, RankProd, stats, utils Suggests: BiocStyle, doFuture, future, knitr, rmarkdown, roxygen2, tinytest License: GPL-3 Package: msmsEDA Version: 1.42.0 Depends: R (>= 3.0.1), MSnbase Imports: MASS, gplots, RColorBrewer License: GPL-2 Package: msmsTests Version: 1.42.0 Depends: R (>= 3.0.1), MSnbase, msmsEDA Imports: edgeR, qvalue Suggests: xtable License: GPL-2 Package: MSnbase Version: 2.30.1 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.7.1), Biobase (>= 2.15.2), mzR (>= 2.29.3), S4Vectors, ProtGenerics (>= 1.29.1) Imports: MsCoreUtils, PSMatch, BiocParallel, IRanges (>= 2.13.28), plyr, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID (>= 1.5.2), digest, lattice, ggplot2, scales, MASS, Rcpp LinkingTo: Rcpp Suggests: testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.7.1), msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, XML, shiny, magrittr, SummarizedExperiment License: Artistic-2.0 Archs: x64 Package: MSnID Version: 1.38.0 Depends: R (>= 2.10), Rcpp Imports: MSnbase (>= 1.12.1), mzID (>= 1.3.5), R.cache, foreach, doParallel, parallel, methods, iterators, data.table, Biobase, ProtGenerics, reshape2, dplyr, mzR, BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics, Biostrings, purrr, rlang, stringr, tibble, AnnotationHub, AnnotationDbi, xtable License: Artistic-2.0 Package: MSPrep Version: 1.14.0 Depends: R (>= 4.1.0) Imports: SummarizedExperiment, S4Vectors, pcaMethods (>= 1.24.0), crmn, preprocessCore, dplyr (>= 0.7), tidyr, tibble (>= 1.2), magrittr, rlang, stats, stringr, methods, missForest, sva, VIM, Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 1.0.2) License: GPL-3 Package: msPurity Version: 1.30.1 Depends: Rcpp Imports: plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW, stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite Suggests: MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA, RPostgres, RMySQL License: GPL-3 + file LICENSE Package: msqrob2 Version: 1.12.0 Depends: R (>= 4.1), QFeatures (>= 1.1.2) Imports: stats, methods, lme4, purrr, BiocParallel, Matrix, MASS, limma, SummarizedExperiment, MultiAssayExperiment, codetools Suggests: multcomp, gridExtra, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown, testthat, tidyverse, plotly, msdata, MSnbase, matrixStats, MsCoreUtils, covr License: Artistic-2.0 Package: MsQuality Version: 1.4.0 Depends: R (>= 4.2.0) Imports: BiocParallel (>= 1.32.0), ggplot2 (>= 3.3.5), htmlwidgets (>= 1.5.3), methods (>= 4.2.0), msdata (>= 0.32.0), MsExperiment (>= 0.99.0), plotly (>= 4.9.4.1), ProtGenerics (>= 1.24.0), rlang (>= 1.1.1), rmzqc (>= 0.5.0), shiny (>= 1.6.0), shinydashboard (>= 0.7.1), Spectra (>= 1.13.2), stats (>= 4.2.0), stringr (>= 1.4.0), tibble (>= 3.1.4), tidyr (>= 1.1.3), utils (>= 4.2.0) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), dplyr (>= 1.0.5), knitr (>= 1.11), mzR (>= 2.32.0), rmarkdown (>= 2.7), S4Vectors (>= 0.29.17), testthat (>= 2.2.1) License: GPL-3 Package: MSstats Version: 4.12.0 Depends: R (>= 4.0) Imports: MSstatsConvert, data.table, checkmate, MASS, htmltools, limma, lme4, preprocessCore, survival, utils, Rcpp, ggplot2, ggrepel, gplots, plotly, marray, stats, grDevices, graphics, methods, statmod, parallel LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, tinytest, covr, markdown License: Artistic-2.0 Archs: x64 Package: MSstatsBig Version: 1.2.0 Imports: arrow, DBI, dplyr, MSstats, MSstatsConvert, readr, sparklyr, utils Suggests: knitr, rmarkdown License: Artistic-2.0 Package: MSstatsConvert Version: 1.14.0 Depends: R (>= 4.0) Imports: data.table, log4r, methods, checkmate, utils, stringi Suggests: tinytest, covr, knitr, rmarkdown License: Artistic-2.0 Package: MSstatsLiP Version: 1.10.0 Depends: R (>= 4.1) Imports: dplyr, gridExtra, stringr, ggplot2, grDevices, MSstats, MSstatsConvert, data.table, Biostrings, MSstatsPTM, Rcpp, checkmate, factoextra, ggpubr, purrr, tibble, tidyr, tidyverse, scales, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight License: Artistic-2.0 Archs: x64 Package: MSstatsLOBD Version: 1.12.0 Depends: R (>= 4.0) Imports: minpack.lm, ggplot2, utils, stats, grDevices LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr License: Artistic-2.0 Package: MSstatsPTM Version: 2.6.0 Depends: R (>= 4.3) Imports: dplyr, gridExtra, stringr, stats, ggplot2, stringi, grDevices, MSstatsTMT, MSstatsConvert, MSstats, data.table, Rcpp, Biostrings, checkmate, ggrepel LinkingTo: Rcpp Suggests: knitr, rmarkdown, tinytest, covr License: Artistic-2.0 Archs: x64 Package: MSstatsQC Version: 2.22.0 Depends: R (>= 3.5.0) Imports: dplyr,plotly,ggplot2,ggExtra, stats,grid, MSnbase, qcmetrics Suggests: knitr,rmarkdown, testthat, RforProteomics License: Artistic License 2.0 Package: MSstatsQCgui Version: 1.24.0 Imports: shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, grid Suggests: knitr License: Artistic License 2.0 Package: MSstatsShiny Version: 1.6.2 Depends: R (>= 4.2) Imports: shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2,plotly, data.table, Hmisc, MSstats, MSstatsTMT, MSstatsPTM, MSstatsConvert, gplots, marray, DT, readxl, ggrepel, uuid, utils, stats, htmltools, methods, tidyr, grDevices, graphics,mockery Suggests: rmarkdown, tinytest, sessioninfo, knitr, testthat (>= 3.0.0), shinytest2, License: Artistic-2.0 Package: MSstatsTMT Version: 2.12.1 Depends: R (>= 4.2) Imports: limma, lme4, lmerTest, methods, data.table, stats, utils, ggplot2, grDevices, graphics, MSstats, MSstatsConvert, checkmate, plotly, htmltools Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 Package: MuData Version: 1.8.0 Depends: Matrix, S4Vectors, rhdf5 Imports: methods, stats, MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, DelayedArray Suggests: HDF5Array, rmarkdown, knitr, fs, testthat, BiocStyle, covr, SingleCellMultiModal, CiteFuse, scater License: GPL-3 Package: Mulcom Version: 1.54.0 Depends: R (>= 2.10), Biobase Imports: graphics, grDevices, stats, methods, fields License: GPL-2 Archs: x64 Package: MultiAssayExperiment Version: 1.30.2 Depends: SummarizedExperiment (>= 1.3.81), R (>= 3.5.0) Imports: Biobase, BiocBaseUtils, BiocGenerics, DelayedArray, GenomicRanges, IRanges, methods, S4Vectors, tidyr, utils Suggests: BiocStyle, HDF5Array, knitr, maftools, R.rsp, RaggedExperiment, reshape2, rmarkdown, survival, survminer, testthat, UpSetR License: Artistic-2.0 Package: MultiBaC Version: 1.14.0 Imports: Matrix, ggplot2, MultiAssayExperiment, ropls, graphics, methods, plotrix, grDevices, pcaMethods Suggests: knitr, rmarkdown, BiocStyle, devtools License: GPL-3 Package: multiClust Version: 1.34.0 Imports: mclust, ctc, survival, cluster, dendextend, amap, graphics, grDevices Suggests: knitr, rmarkdown, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery License: GPL (>= 2) Package: multicrispr Version: 1.14.0 Depends: R (>= 4.0) Imports: BiocGenerics, Biostrings, BSgenome, CRISPRseek, data.table, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, grid, karyoploteR, magrittr, methods, parallel, plyranges, Rbowtie, reticulate, rtracklayer, stats, stringi, tidyr, tidyselect, utils Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer1, ensembldb, IRanges, knitr, magick, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL-2 Package: MultiDataSet Version: 1.32.0 Depends: R (>= 4.1), Biobase Imports: BiocGenerics, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, methods, utils, ggplot2, ggrepel, qqman, limma Suggests: brgedata, minfi, minfiData, knitr, rmarkdown, testthat, omicade4, iClusterPlus, GEOquery, MultiAssayExperiment, BiocStyle, RaggedExperiment License: file LICENSE Package: multiGSEA Version: 1.14.0 Depends: R (>= 4.0.0) Imports: magrittr, graphite, AnnotationDbi, metaboliteIDmapping, dplyr, fgsea, metap, rappdirs, rlang, methods Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Ss.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Xl.eg.db, org.Cf.eg.db, knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0) License: GPL-3 Package: multiHiCcompare Version: 1.22.0 Depends: R (>= 4.0.0) Imports: data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, GenomeInfoDb, aggregation Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE Package: MultiMed Version: 2.26.0 Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: GPL (>= 2) + file LICENSE Package: multiMiR Version: 1.26.0 Depends: R (>= 3.4) Imports: stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 1.2), methods, BiocGenerics, AnnotationDbi, dplyr, Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2) License: MIT + file LICENSE Package: MultimodalExperiment Version: 1.4.0 Depends: R (>= 4.3.0), IRanges, S4Vectors Imports: BiocGenerics, MultiAssayExperiment, methods, utils Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 Package: multiOmicsViz Version: 1.28.0 Depends: R (>= 3.3.2) Imports: methods, parallel, doParallel, foreach, grDevices, graphics, utils, SummarizedExperiment, stats Suggests: BiocGenerics License: LGPL Package: MultiRNAflow Version: 1.2.0 Depends: Mfuzz (>= 2.58.0), R (>= 4.3) Imports: Biobase (>= 2.54.0), ComplexHeatmap (>= 2.14.0), DESeq2 (>= 1.38.1), factoextra (>= 1.0.7), FactoMineR (>= 2.6), ggalluvial (>= 0.12.3), ggplot2 (>= 3.4.0), ggplotify (>= 0.1.2), ggrepel (>= 0.9.2), gprofiler2 (>= 0.2.1), graphics (>= 4.2.2), grDevices (>= 4.2.2), grid (>= 4.2.2), plot3D (>= 1.4), plot3Drgl (>= 1.0.3), reshape2 (>= 1.4.4), S4Vectors (>= 0.36.2), stats (>= 4.2.2), SummarizedExperiment (>= 1.28.0), UpSetR (>= 1.4.0), utils (>= 4.2.2) Suggests: BiocGenerics (>= 0.40.0), BiocStyle, e1071 (>= 1.7.12), knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 | file LICENSE Package: multiscan Version: 1.64.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) Archs: x64 Package: multistateQTL Version: 1.0.0 Depends: QTLExperiment, SummarizedExperiment, ComplexHeatmap, data.table, collapse Imports: methods, S4Vectors, grid, dplyr, tidyr, matrixStats, stats, fitdistrplus, viridis, ggplot2, circlize, mashr, grDevices Suggests: testthat, BiocStyle, knitr, covr, rmarkdown License: GPL-3 Package: multiWGCNA Version: 1.2.0 Depends: R (>= 4.3.0), ggalluvial Imports: stringr, readr, WGCNA, dplyr, reshape2, data.table, patchwork, scales, igraph, flashClust, ggplot2, dcanr, cowplot, ggrepel, methods, SummarizedExperiment Suggests: BiocStyle, doParallel, ExperimentHub, knitr, markdown, rmarkdown, testthat (>= 3.0.0), vegan License: GPL-3 Package: multtest Version: 2.60.0 Depends: R (>= 2.10), methods, BiocGenerics, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL Archs: x64 Package: mumosa Version: 1.12.0 Depends: SingleCellExperiment Imports: stats, utils, methods, igraph, Matrix, BiocGenerics, BiocParallel, IRanges, S4Vectors, DelayedArray, DelayedMatrixStats, SummarizedExperiment, BiocNeighbors, BiocSingular, ScaledMatrix, beachmat, scuttle, metapod, scran, batchelor, uwot Suggests: testthat, knitr, BiocStyle, rmarkdown, scater, bluster, DropletUtils, scRNAseq License: GPL-3 Package: MungeSumstats Version: 1.12.0 Depends: R(>= 4.1) Imports: magrittr, data.table, utils, R.utils, dplyr, stats, GenomicRanges, IRanges, GenomeInfoDb, BSgenome, Biostrings, stringr, VariantAnnotation, googleAuthR, httr, jsonlite, methods, parallel, rtracklayer(>= 1.59.1), RCurl Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr, Rsamtools, MatrixGenerics, badger, BiocParallel, GenomicFiles License: Artistic-2.0 Package: muscat Version: 1.18.0 Depends: R (>= 4.3) Imports: BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, Matrix, matrixStats, methods, progress, purrr, S4Vectors, scales, scater, scuttle, sctransform, stats, SingleCellExperiment, SummarizedExperiment, variancePartition, viridis Suggests: BiocStyle, countsimQC, cowplot, ExperimentHub, iCOBRA, knitr, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, testthat, UpSetR License: GPL-3 Package: muscle Version: 3.46.0 Depends: Biostrings License: Unlimited Archs: x64 Package: musicatk Version: 1.14.0 Depends: R (>= 4.0.0), NMF Imports: SummarizedExperiment, VariantAnnotation, Biostrings, base, methods, magrittr, tibble, tidyr, gtools, gridExtra, MCMCprecision, MASS, matrixTests, data.table, dplyr, rlang, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, S4Vectors, uwot, ggplot2, stringr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, deconstructSigs, decompTumor2Sig, topicmodels, ggrepel, plotly, utils, factoextra, cluster, ComplexHeatmap, philentropy, maftools, shiny, stringi, tidyverse, ggpubr, Matrix (>= 1.6.1) Suggests: TCGAbiolinks, shinyBS, shinyalert, shinybusy, shinydashboard, shinyjs, shinyjqui, sortable, testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr, shinyWidgets, cowplot, withr License: LGPL-3 Package: MutationalPatterns Version: 3.14.0 Depends: R (>= 4.2.0), GenomicRanges (>= 1.24.0), NMF (>= 0.20.6) Imports: stats, S4Vectors, BiocGenerics (>= 0.18.0), BSgenome (>= 1.40.0), VariantAnnotation (>= 1.18.1), dplyr (>= 0.8.3), tibble(>= 2.1.3), purrr (>= 0.3.2), tidyr (>= 1.0.0), stringr (>= 1.4.0), magrittr (>= 1.5), ggplot2 (>= 2.1.0), pracma (>= 1.8.8), IRanges (>= 2.6.0), GenomeInfoDb (>= 1.12.0), Biostrings (>= 2.40.0), ggdendro (>= 0.1-20), cowplot (>= 0.9.2), ggalluvial (>= 0.12.2), RColorBrewer, methods Suggests: BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BiocStyle (>= 2.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), biomaRt (>= 2.28.0), gridExtra (>= 2.2.1), rtracklayer (>= 1.32.2), ccfindR (>= 1.6.0), GenomicFeatures, AnnotationDbi, testthat, knitr, rmarkdown License: MIT + file LICENSE Package: MVCClass Version: 1.78.0 Depends: R (>= 2.1.0), methods License: LGPL Package: MWASTools Version: 1.28.0 Depends: R (>= 3.5.0) Imports: glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra, igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST, ComplexHeatmap, stats, utils Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: CC BY-NC-ND 4.0 Package: mygene Version: 1.40.0 Depends: R (>= 3.2.1), GenomicFeatures, txdbmaker Imports: methods, utils, stats, httr (>= 0.3), jsonlite (>= 0.9.7), Hmisc, sqldf, plyr, S4Vectors Suggests: BiocStyle License: Artistic-2.0 Package: myvariant Version: 1.34.0 Depends: R (>= 3.2.1), VariantAnnotation Imports: httr, jsonlite, S4Vectors, Hmisc, plyr, magrittr, GenomeInfoDb Suggests: BiocStyle License: Artistic-2.0 Package: mzID Version: 1.42.0 Depends: methods Imports: XML, plyr, parallel, doParallel, foreach, iterators, ProtGenerics Suggests: knitr, testthat License: GPL (>= 2) Package: mzR Version: 2.38.0 Depends: R (>= 4.0.0), Rcpp (>= 0.10.1), methods, utils Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3), ncdf4 LinkingTo: Rcpp, Rhdf5lib (>= 1.1.4) Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML, rmarkdown License: Artistic-2.0 Archs: x64 Package: NADfinder Version: 1.28.0 Depends: R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges, S4Vectors, SummarizedExperiment Imports: graphics, methods, baseline, signal, GenomicAlignments, GenomeInfoDb, rtracklayer, limma, trackViewer, stats, utils, Rsamtools, metap, EmpiricalBrownsMethod,ATACseqQC, corrplot, csaw Suggests: RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat, BiocManager, rmarkdown License: GPL (>= 2) Package: NanoMethViz Version: 3.0.2 Depends: R (>= 4.0.0), methods, ggplot2 (>= 3.4.0) Imports: cpp11 (>= 0.2.5), readr, cli, S4Vectors, SummarizedExperiment, BiocSingular, bsseq, forcats, assertthat, AnnotationDbi, Rcpp, dplyr, data.table, dbscan, e1071, fs, GenomicRanges, Biostrings, ggrastr, glue, graphics, IRanges, limma (>= 3.44.0), patchwork, purrr, rlang, R.utils, Rsamtools, scales (>= 1.2.0), scico, stats, stringr, tibble, tidyr, utils, withr, zlibbioc LinkingTo: Rcpp Suggests: BiocStyle, DSS, Mus.musculus (>= 1.3.1), Homo.sapiens (>= 1.3.1), org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm39.refGene, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0), covr License: Apache License (>= 2.0) Archs: x64 Package: NanoStringDiff Version: 1.34.0 Depends: Biobase Imports: matrixStats, methods, Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle License: GPL Archs: x64 Package: NanoStringNCTools Version: 1.12.0 Depends: R (>= 3.6), Biobase, S4Vectors, ggplot2 Imports: BiocGenerics, Biostrings, ggbeeswarm, ggiraph, ggthemes, grDevices, IRanges, methods, pheatmap, RColorBrewer, stats, utils Suggests: biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf License: MIT Package: NanoTube Version: 1.10.0 Depends: R (>= 4.1), Biobase, ggplot2, limma Imports: fgsea, methods, reshape, stats, utils Suggests: grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly, rlang, rmarkdown, ruv, RUVSeq, shiny, testthat, xlsx License: GPL-3 + file LICENSE Package: NBAMSeq Version: 1.20.0 Depends: R (>= 3.6), SummarizedExperiment, S4Vectors Imports: DESeq2, mgcv(>= 1.8-24), BiocParallel, genefilter, methods, stats, Suggests: knitr, rmarkdown, testthat, ggplot2 License: GPL-2 Package: ncdfFlow Version: 2.50.0 Depends: R (>= 2.14.0), flowCore(>= 1.51.7), methods, BH Imports: Biobase,BiocGenerics,flowCore,zlibbioc LinkingTo: cpp11,BH, Rhdf5lib Suggests: testthat,parallel,flowStats,knitr Archs: x64 Package: ncGTW Version: 1.18.0 Depends: methods, BiocParallel, xcms Imports: Rcpp, grDevices, graphics, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, rmarkdown License: GPL-2 Archs: x64 Package: ncRNAtools Version: 1.14.0 Imports: httr, xml2, utils, methods, grDevices, ggplot2, IRanges, GenomicRanges, S4Vectors Suggests: knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics License: GPL-3 Package: ndexr Version: 1.26.0 Depends: RCX Imports: httr, jsonlite, plyr, tidyr Suggests: BiocStyle, testthat, knitr, rmarkdown License: BSD_3_clause + file LICENSE Package: nearBynding Version: 1.14.0 Depends: R (>= 4.0) Imports: R.utils, matrixStats, plyranges, transport, Rsamtools, S4Vectors, grDevices, graphics, rtracklayer, dplyr, GenomeInfoDb, methods, GenomicRanges, utils, stats, magrittr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, ggplot2, gplots, BiocGenerics, rlang Suggests: knitr, rmarkdown License: Artistic-2.0 Package: Nebulosa Version: 1.14.0 Depends: R (>= 4.0), ggplot2, patchwork Imports: SingleCellExperiment, SummarizedExperiment, SeuratObject, ks, Matrix, stats, methods, ggrastr Suggests: testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils, igraph, BiocFileCache, Seurat License: GPL-3 Package: NeighborNet Version: 1.22.0 Depends: methods Imports: graph, stats License: CC BY-NC-ND 4.0 Package: nempi Version: 1.12.0 Depends: R (>= 4.1), mnem Imports: e1071, nnet, randomForest, naturalsort, graphics, stats, utils, matrixStats, epiNEM Suggests: knitr, BiocGenerics, rmarkdown, RUnit, BiocStyle License: GPL-3 Package: NetActivity Version: 1.6.0 Depends: R (>= 4.1.0) Imports: airway, DelayedArray, DelayedMatrixStats, DESeq2, methods, methods, NetActivityData, SummarizedExperiment, utils Suggests: AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0), tidyverse License: MIT + file LICENSE Package: nethet Version: 1.36.0 Imports: glasso, mvtnorm, GeneNet, huge, CompQuadForm, ggm, mclust, parallel, GSA, limma, multtest, ICSNP, glmnet, network, ggplot2, grDevices, graphics, stats, utils Suggests: knitr, xtable, BiocStyle, testthat License: GPL-2 Archs: x64 Package: NetPathMiner Version: 1.40.0 Depends: R (>= 3.0.2), igraph (>= 1.0) Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle License: GPL (>= 2) Archs: x64 Package: netprioR Version: 1.30.0 Depends: methods, graphics, R(>= 3.3) Imports: stats, Matrix, dplyr, doParallel, foreach, parallel, sparseMVN, ggplot2, gridExtra, pROC Suggests: knitr, BiocStyle, pander License: GPL-3 Package: netresponse Version: 1.64.0 Depends: R (>= 2.15.1), BiocStyle, Rgraphviz, rmarkdown, methods, minet, mclust, reshape2 Imports: ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer Suggests: knitr License: GPL (>= 2) Archs: x64 Package: NetSAM Version: 1.44.0 Depends: R (>= 3.0.0), seriation (>= 1.0-6), igraph (>= 2.0.0), tools (>= 3.0.0), WGCNA (>= 1.34.0), biomaRt (>= 2.18.0) Imports: methods, AnnotationDbi (>= 1.28.0), doParallel (>= 1.0.10), foreach (>= 1.4.0), survival (>= 2.37-7), GO.db (>= 2.10.0), R2HTML (>= 2.2.0), DBI (>= 0.5-1) Suggests: RUnit, BiocGenerics, org.Sc.sgd.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dr.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.At.tair.db, rmarkdown, knitr, markdown License: LGPL Package: netSmooth Version: 1.24.0 Depends: R (>= 3.5), scater (>= 1.15.11), clusterExperiment (>= 2.1.6) Imports: entropy, SummarizedExperiment, SingleCellExperiment, Matrix, cluster, data.table, stats, methods, DelayedArray, HDF5Array (>= 1.15.13) Suggests: knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot License: GPL-3 Package: netZooR Version: 1.8.0 Depends: R (>= 4.2.0), igraph, reticulate, pandaR, yarn, matrixcalc Imports: RCy3, viridisLite, STRINGdb, Biobase, GOstats, AnnotationDbi, matrixStats, GO.db, org.Hs.eg.db, Matrix, gplots, nnet, data.table, vegan, stats, utils, reshape, reshape2, penalized, parallel, doParallel, foreach, ggplot2, ggdendro, grid, MASS, assertthat, tidyr, methods, dplyr, graphics Suggests: testthat (>= 2.1.0), knitr, rmarkdown, pkgdown License: GPL-3 Package: NeuCA Version: 1.10.0 Depends: R(>= 3.5.0), keras, limma, e1071, SingleCellExperiment, kableExtra Suggests: BiocStyle, knitr, rmarkdown, networkD3 License: GPL-2 Package: NewWave Version: 1.14.0 Depends: R (>= 4.0), SummarizedExperiment Imports: methods, SingleCellExperiment, parallel, irlba, Matrix, DelayedArray, BiocSingular, SharedObject, stats Suggests: testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr License: GPL-3 Package: ngsReports Version: 2.6.0 Depends: R (>= 4.2.0), BiocGenerics, ggplot2 (>= 3.5.0), patchwork (>= 1.1.1), tibble (>= 1.3.1) Imports: Biostrings, checkmate, dplyr (>= 1.1.0), forcats, ggdendro, grDevices (>= 3.6.0), grid, jsonlite, lifecycle, lubridate, methods, plotly (>= 4.9.4), reshape2, rlang, rmarkdown, scales, stats, stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo Suggests: BiocStyle, Cairo, DT, knitr, pander, readr, testthat, truncnorm License: LGPL-3 Package: nipalsMCIA Version: 1.2.0 Depends: R (>= 4.3.0) Imports: ComplexHeatmap, dplyr, fgsea, ggplot2 (>= 3.0.0), graphics, grid, methods, MultiAssayExperiment, SummarizedExperiment, pracma, rlang, RSpectra, scales, stats Suggests: BiocFileCache, BiocStyle, circlize, ggpubr, KernSmooth, knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>= 4.0.0), spatstat.explore, stringr, survival, tidyverse, testthat (>= 3.0.0) License: GPL-3 Package: nnNorm Version: 2.68.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL Package: nnSVG Version: 1.8.0 Depends: R (>= 4.2) Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, BRISC, BiocParallel, Matrix, matrixStats, stats, methods Suggests: BiocStyle, knitr, rmarkdown, STexampleData, WeberDivechaLCdata, scran, ggplot2, testthat License: MIT + file LICENSE Package: NOISeq Version: 2.48.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2) License: Artistic-2.0 Package: NoRCE Version: 1.16.0 Depends: R (>= 4.2.0) Imports: KEGGREST,png,dplyr,graphics,RSQLite,DBI,tidyr,grDevices,stringr,GenomeInfoDb, S4Vectors,SummarizedExperiment,reactome.db,rWikiPathways,RCurl, dbplyr,utils,ggplot2,igraph,stats,reshape2,readr, GO.db,zlibbioc, biomaRt,rtracklayer,IRanges,GenomicRanges,GenomicFeatures,AnnotationDbi Suggests: knitr, TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene, testthat,TxDb.Celegans.UCSC.ce11.refGene,rmarkdown, TxDb.Rnorvegicus.UCSC.rn6.refGene,TxDb.Hsapiens.UCSC.hg19.knownGene, org.Mm.eg.db, org.Rn.eg.db,org.Hs.eg.db,org.Dr.eg.db,BiocGenerics, org.Sc.sgd.db, org.Ce.eg.db,org.Dm.eg.db, methods,markdown License: MIT + file LICENSE Package: normalize450K Version: 1.32.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE Package: NormalyzerDE Version: 1.22.0 Depends: R (>= 4.1.0) Imports: vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, Biobase, utils, stats, SummarizedExperiment, matrixStats, ggforce Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle License: Artistic-2.0 Package: NormqPCR Version: 1.50.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR License: LGPL-3 Package: normr Version: 1.30.0 Depends: R (>= 3.3.0) Imports: methods, stats, utils, grDevices, parallel, GenomeInfoDb, GenomicRanges, IRanges, Rcpp (>= 0.11), qvalue (>= 2.2), bamsignals (>= 1.4), rtracklayer (>= 1.32) LinkingTo: Rcpp Suggests: BiocStyle, testthat (>= 1.0), knitr, rmarkdown Enhances: BiocParallel License: GPL-2 Archs: x64 Package: NPARC Version: 1.16.0 Depends: R (>= 4.0.0) Imports: dplyr, tidyr, BiocParallel, broom, MASS, rlang, magrittr, stats, methods Suggests: testthat, devtools, knitr, rprojroot, rmarkdown, ggplot2, BiocStyle License: GPL-3 Package: npGSEA Version: 1.40.0 Depends: GSEABase (>= 1.24.0) Imports: Biobase, methods, BiocGenerics, graphics, stats Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle License: Artistic-2.0 Package: NTW Version: 1.54.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 Package: nucleoSim Version: 1.32.0 Imports: stats, IRanges, S4Vectors, graphics, methods Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, testthat License: Artistic-2.0 Package: nucleR Version: 2.36.0 Depends: R (>= 3.5.0), methods Imports: Biobase, BiocGenerics, Biostrings, GenomeInfoDb, GenomicRanges, IRanges, Rsamtools, S4Vectors, ShortRead, dplyr, ggplot2, magrittr, parallel, stats, utils, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat License: LGPL (>= 3) Package: nuCpos Version: 1.22.0 Depends: R (>= 4.2.0) Imports: graphics, methods Suggests: NuPoP, Biostrings, testthat License: GPL-2 Package: nullranges Version: 1.10.0 Imports: stats, IRanges, GenomicRanges, GenomeInfoDb, methods, rlang, S4Vectors, scales, InteractionSet, ggplot2, grDevices, plyranges, data.table, progress, ggridges Suggests: testthat, knitr, rmarkdown, ks, DNAcopy, RcppHMM, AnnotationHub, ExperimentHub, nullrangesData, excluderanges, ensembldb, EnsDb.Hsapiens.v86, BSgenome.Hsapiens.UCSC.hg38, patchwork, plotgardener, dplyr, purrr, magrittr, tidyr, cobalt, DiagrammeR, tidySummarizedExperiment License: GPL-3 Package: NuPoP Version: 2.12.0 Depends: R (>= 4.0) Imports: graphics, utils Suggests: knitr, rmarkdown License: GPL-2 Archs: x64 Package: occugene Version: 1.64.0 Depends: R (>= 2.0.0) License: GPL (>= 2) Package: OCplus Version: 1.78.0 Depends: R (>= 2.1.0) Imports: multtest (>= 1.7.3), graphics, grDevices, stats, interp License: LGPL Package: octad Version: 1.6.0 Depends: R (>= 4.2.0), magrittr, dplyr, ggplot2, edgeR, RUVSeq, DESeq2, limma, rhdf5, foreach, Rfast, octad.db, stats, httr, qpdf, ExperimentHub, AnnotationHub, Biobase, S4Vectors Imports: EDASeq, GSVA, data.table, htmlwidgets, plotly, reshape2, grDevices, utils Suggests: knitr, rmarkdown License: Artistic-2.0 Package: odseq Version: 1.32.0 Depends: R (>= 3.2.3) Imports: msa (>= 1.2.1), kebabs (>= 1.4.1), mclust (>= 5.1) Suggests: knitr(>= 1.11) License: MIT + file LICENSE Package: OGRE Version: 1.8.0 Depends: R (>= 4.2.0), S4Vectors Imports: GenomicRanges, methods, data.table, assertthat, ggplot2, Gviz, IRanges, AnnotationHub, grDevices, stats, GenomeInfoDb, shiny, shinyFiles, DT, rtracklayer, shinydashboard, shinyBS,tidyr Suggests: testthat (>= 3.0.0), knitr (>= 1.36), rmarkdown (>= 2.11) License: Artistic-2.0 Package: oligo Version: 1.68.2 Depends: R (>= 3.2.0), BiocGenerics (>= 0.13.11), oligoClasses (>= 1.29.6), Biobase (>= 2.27.3), Biostrings (>= 2.35.12) Imports: affyio (>= 1.35.0), affxparser (>= 1.39.4), DBI (>= 0.3.1), ff, graphics, methods, preprocessCore (>= 1.29.0), RSQLite (>= 1.0.0), splines, stats, stats4, utils, zlibbioc LinkingTo: preprocessCore Suggests: BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, ACME, RCurl Enhances: doMC, doMPI License: LGPL (>= 2) Archs: x64 Package: oligoClasses Version: 1.66.0 Depends: R (>= 2.14) Imports: BiocGenerics (>= 0.27.1), Biobase (>= 2.17.8), methods, graphics, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>= 1.23.2), foreach, BiocManager, utils, S4Vectors (>= 0.9.25), RSQLite, DBI, ff Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), RUnit, human370v1cCrlmm, VanillaICE, crlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: GPL (>= 2) Package: OLIN Version: 1.82.0 Depends: R (>= 2.10), methods, locfit, marray Imports: graphics, grDevices, limma, marray, methods, stats Suggests: convert License: GPL-2 Package: OLINgui Version: 1.78.0 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Imports: graphics, marray, OLIN, tcltk, tkWidgets, widgetTools License: GPL-2 Package: omada Version: 1.6.0 Depends: pdfCluster (>= 1.0-3), kernlab (>= 0.9-29), R (>= 4.2), fpc (>= 2.2-9), Rcpp (>= 1.0.7), diceR (>= 0.6.0), ggplot2 (>= 3.3.5), reshape (>= 0.8.8), genieclust (>= 1.1.3), clValid (>= 0.7), glmnet (>= 4.1.3), dplyr(>= 1.0.7), stats (>= 4.1.2), clValid(>= 0.7) Suggests: rmarkdown, knitr, testthat License: GPL-3 Package: OmaDB Version: 2.20.0 Depends: R (>= 3.5), httr (>= 1.2.1), plyr(>= 1.8.4) Imports: utils, ape, Biostrings, GenomicRanges, IRanges, methods, topGO, jsonlite Suggests: knitr, rmarkdown, testthat License: GPL-3 Package: omicade4 Version: 1.44.0 Depends: R (>= 3.0.0), ade4 Imports: made4, Biobase Suggests: BiocStyle License: GPL-2 Package: OmicCircos Version: 1.42.0 Depends: R (>= 2.14.0), methods,GenomicRanges License: GPL-2 Package: omicplotR Version: 1.24.0 Depends: R (>= 3.6), ALDEx2 (>= 1.18.0) Imports: compositions, DT, grDevices, knitr, jsonlite, matrixStats, rmarkdown, shiny, stats, vegan, zCompositions License: MIT + file LICENSE Package: omicRexposome Version: 1.26.0 Depends: R (>= 3.5.0), Biobase Imports: stats, utils, grDevices, graphics, methods, rexposome, limma, sva, ggplot2, ggrepel, PMA, omicade4, gridExtra, MultiDataSet, SmartSVA, isva, parallel, SummarizedExperiment, stringr Suggests: BiocStyle, knitr, rmarkdown, snpStats, brgedata License: MIT + file LICENSE Package: OMICsPCA Version: 1.22.0 Depends: R (>= 3.5.0), OMICsPCAdata Imports: HelloRanges, fpc, stats, MultiAssayExperiment, pdftools, methods, grDevices, utils,clValid, NbClust, cowplot, rmarkdown, kableExtra, rtracklayer, IRanges, GenomeInfoDb, reshape2, ggplot2, factoextra, rgl, corrplot, MASS, graphics, FactoMineR, PerformanceAnalytics, tidyr, data.table, cluster, magick Suggests: knitr, RUnit, BiocGenerics License: GPL-3 Package: omicsPrint Version: 1.24.0 Depends: R (>= 3.5), MASS Imports: methods, matrixStats, graphics, stats, SummarizedExperiment, MultiAssayExperiment, RaggedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats License: GPL (>= 2) Package: omicsViewer Version: 1.8.0 Depends: R (>= 4.2) Imports: survminer, survival, fastmatch, reshape2, stringr, beeswarm, grDevices, DT, shiny, shinythemes, shinyWidgets, plotly, networkD3, httr, matrixStats, RColorBrewer, Biobase, fgsea, openxlsx, psych, shinybusy, ggseqlogo, htmlwidgets, graphics, grid, stats, utils, methods, shinyjs, curl, flatxml, ggplot2, S4Vectors, SummarizedExperiment, RSQLite, Matrix, shinycssloaders, ROCR, drc Suggests: BiocStyle, knitr, rmarkdown, unittest License: GPL-2 Package: Omixer Version: 1.14.0 Depends: R (>= 4.0.0) Imports: dplyr, ggplot2, forcats, tibble, gridExtra, magrittr, readr, tidyselect, grid, stats, stringr Suggests: knitr, rmarkdown, BiocStyle, magick, testthat License: MIT + file LICENSE Package: OmnipathR Version: 3.11.10 Depends: R(>= 4.0) Imports: checkmate, crayon, curl, digest, dplyr(>= 1.1.0), httr, igraph, jsonlite, later, logger, lubridate, magrittr, progress, purrr, rappdirs, readr(>= 2.0.0), readxl, rlang, rmarkdown, rvest, stats, stringi, stringr, tibble, tidyr, tidyselect, tools, utils, withr, xml2, yaml Suggests: BiocStyle, biomaRt, bookdown, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, sigmajs, smoof, supraHex, testthat License: MIT + file LICENSE Package: ompBAM Version: 1.8.0 Imports: utils, Rcpp, zlibbioc Suggests: RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis, desc, testthat (>= 3.0.0) License: MIT + file LICENSE Package: oncomix Version: 1.26.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, RMySQL License: GPL-3 Package: oncoscanR Version: 1.6.0 Depends: R (>= 4.2), IRanges (>= 2.30.0), GenomicRanges (>= 1.48.0), magrittr Imports: readr, S4Vectors, methods, utils Suggests: testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE Package: OncoScore Version: 1.32.0 Depends: R (>= 4.1.0), Imports: biomaRt, grDevices, graphics, utils, methods, Suggests: BiocGenerics, BiocStyle, knitr, testthat, License: file LICENSE Package: OncoSimulR Version: 4.6.0 Depends: R (>= 3.5.0) Imports: Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz, gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr, smatr, ggplot2, ggrepel, stringr LinkingTo: Rcpp Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander License: GPL (>= 3) Archs: x64 Package: onlineFDR Version: 2.12.0 Imports: stats, Rcpp, progress LinkingTo: Rcpp, RcppProgress Suggests: knitr, rmarkdown, testthat, covr License: GPL-3 Archs: x64 Package: ontoProc Version: 1.26.0 Depends: R (>= 4.0), ontologyIndex Imports: Biobase, S4Vectors, methods, stats, utils, BiocFileCache, shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT, igraph, AnnotationHub, SummarizedExperiment, reticulate, R.utils, httr Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown, AnnotationDbi License: Artistic-2.0 Package: openCyto Version: 2.16.1 Depends: R (>= 3.5.0) Imports: methods,Biobase,BiocGenerics,flowCore(>= 1.99.17),flowViz,ncdfFlow(>= 2.11.34),flowWorkspace(>= 3.99.1),flowClust(>= 3.11.4),RBGL,graph,data.table,RColorBrewer LinkingTo: cpp11, BH Suggests: flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2), MASS Archs: x64 Package: openPrimeR Version: 1.26.0 Depends: R (>= 4.0.0) Imports: Biostrings (>= 2.38.4), pwalign, XML (>= 3.98-1.4), scales (>= 0.4.0), reshape2 (>= 1.4.1), seqinr (>= 3.3-3), IRanges (>= 2.4.8), GenomicRanges (>= 1.22.4), ggplot2 (>= 2.1.0), plyr (>= 1.8.4), dplyr (>= 0.5.0), stringdist (>= 0.9.4.1), stringr (>= 1.0.0), RColorBrewer (>= 1.1-2), DECIPHER (>= 1.16.1), lpSolveAPI (>= 5.5.2.0-17), digest (>= 0.6.9), Hmisc (>= 3.17-4), ape (>= 3.5), BiocGenerics (>= 0.16.1), S4Vectors (>= 0.8.11), foreach (>= 1.4.3), magrittr (>= 1.5), uniqtag (>= 1.0), openxlsx (>= 4.0.17), grid (>= 3.1.0), grDevices (>= 3.1.0), stats (>= 3.1.0), utils (>= 3.1.0), methods (>= 3.1.0) Suggests: testthat (>= 1.0.2), knitr (>= 1.13), rmarkdown (>= 1.0), devtools (>= 1.12.0), doParallel (>= 1.0.10), pander (>= 0.6.0), learnr (>= 0.9) License: GPL-2 Package: openPrimeRui Version: 1.26.0 Depends: R (>= 4.0.0), openPrimeR (>= 0.99.0) Imports: shiny (>= 1.0.2), shinyjs (>= 0.9), shinyBS (>= 0.61), DT (>= 0.2), rmarkdown (>= 1.0) Suggests: knitr (>= 1.13) License: GPL-2 Package: OpenStats Version: 1.16.0 Depends: nlme Imports: MASS, jsonlite, Hmisc, methods, knitr, AICcmodavg, car, rlist, summarytools, graphics, stats, utils Suggests: rmarkdown License: GPL (>= 2) Package: oposSOM Version: 2.22.0 Depends: R (>= 4.0.0), igraph (>= 1.0.0) Imports: fastICA, tsne, scatterplot3d, pixmap, fdrtool, ape, biomaRt, Biobase, RcppParallel, Rcpp, methods, graph, XML, png, RCurl LinkingTo: RcppParallel, Rcpp License: GPL (>= 2) Archs: x64 Package: oppar Version: 1.32.0 Depends: R (>= 3.3) Imports: Biobase, methods, GSEABase, GSVA Suggests: knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel License: GPL-2 Archs: x64 Package: oppti Version: 1.18.0 Depends: R (>= 3.5) Imports: limma, stats, reshape, ggplot2, grDevices, RColorBrewer, pheatmap, knitr, methods, devtools, parallelDist, Suggests: markdown License: MIT Package: optimalFlow Version: 1.16.0 Depends: dplyr, optimalFlowData, rlang (>= 0.4.0) Imports: transport, parallel, Rfast, robustbase, dbscan, randomForest, foreach, graphics, doParallel, stats, flowMeans, rgl, ellipse Suggests: knitr, BiocStyle, rmarkdown, magick License: Artistic-2.0 Package: OPWeight Version: 1.26.0 Depends: R (>= 3.4.0), Imports: graphics, qvalue, MASS, tibble, stats, Suggests: airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2, gridExtra, knitr, Matrix, rmarkdown, scales, testthat License: Artistic-2.0 Package: OrderedList Version: 1.76.0 Depends: R (>= 3.6.1), Biobase, twilight Imports: methods License: GPL (>= 2) Package: ORFhunteR Version: 1.12.0 Depends: Biostrings, rtracklayer, Peptides Imports: Rcpp (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg38, data.table, stringr, randomForest, xfun, stats, utils, parallel, graphics LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown License: MIT License Archs: x64 Package: ORFik Version: 1.24.0 Depends: R (>= 4.4.0), IRanges (>= 2.17.1), GenomicRanges (>= 1.35.1), GenomicAlignments (>= 1.19.0) Imports: AnnotationDbi (>= 1.45.0), Biostrings (>= 2.51.1), biomaRt, biomartr (>= 1.0.7), BiocFileCache, BiocGenerics (>= 0.29.1), BiocParallel (>= 1.19.0), BSgenome, cowplot (>= 1.0.0), curl, RCurl, data.table (>= 1.11.8), DESeq2 (>= 1.24.0), downloader, fst (>= 0.9.2), GenomeInfoDb (>= 1.15.5), GenomicFeatures (>= 1.31.10), ggplot2 (>= 2.2.1), gridExtra (>= 2.3), httr (>= 1.3.0), jsonlite, methods (>= 3.6.0), R.utils, Rcpp (>= 1.0.0), Rsamtools (>= 1.35.0), rtracklayer (>= 1.43.0), stats, SummarizedExperiment (>= 1.14.0), S4Vectors (>= 0.21.3), tools, txdbmaker, utils, XML, xml2 (>= 1.2.0), withr LinkingTo: Rcpp Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE Archs: x64 Package: OrganismDbi Version: 1.46.0 Depends: R (>= 2.14.0), BiocGenerics (>= 0.15.10), AnnotationDbi (>= 1.33.15), GenomicFeatures (>= 1.39.4) Imports: methods, utils, stats, DBI, BiocManager, Biobase, graph, RBGL, S4Vectors, IRanges, GenomicRanges (>= 1.31.13), txdbmaker Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, rtracklayer, biomaRt, RUnit, RMariaDB, BiocStyle, knitr License: Artistic-2.0 Package: Organism.dplyr Version: 1.32.0 Depends: R (>= 3.4), dplyr (>= 0.7.0), AnnotationFilter (>= 1.1.3) Imports: RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges, GenomicFeatures, AnnotationDbi, rlang, methods, tools, utils, BiocFileCache, DBI, dbplyr, tibble Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, magick, BiocStyle, ggplot2 License: Artistic-2.0 Package: orthogene Version: 1.10.0 Depends: R (>= 4.1) Imports: dplyr, methods, stats, utils, Matrix, jsonlite, homologene, gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr, patchwork, DelayedArray, grr, repmis, ggtree, tools Suggests: rworkflows, remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB License: GPL-3 Package: orthos Version: 1.2.0 Depends: R (>= 4.3), SummarizedExperiment Imports: AnnotationHub, basilisk, BiocParallel, colorspace, cowplot, DelayedArray, dplyr, ExperimentHub, ggplot2, ggpubr, ggrepel, ggsci, grDevices, grid, HDF5Array, keras, methods, orthosData, parallel, plyr, reticulate, rlang, S4Vectors, stats, tensorflow, tidyr Suggests: BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE Package: OSAT Version: 1.52.0 Depends: methods,stats Suggests: xtable, Biobase License: Artistic-2.0 Package: Oscope Version: 1.34.0 Depends: EBSeq, cluster, testthat, BiocParallel Suggests: BiocStyle License: Artistic-2.0 Package: OTUbase Version: 1.54.0 Depends: R (>= 2.9.0), methods, S4Vectors, IRanges, ShortRead (>= 1.23.15), Biobase, vegan Imports: Biostrings License: Artistic-2.0 Package: OUTRIDER Version: 1.22.0 Depends: R (>= 3.6), BiocParallel, GenomicFeatures, SummarizedExperiment, data.table, methods Imports: BBmisc, BiocGenerics, DESeq2 (>= 1.16.1), generics, GenomicRanges, ggplot2, ggrepel, grDevices, heatmaply, pheatmap, graphics, IRanges, matrixStats, plotly, plyr, pcaMethods, PRROC, RColorBrewer, reshape2, S4Vectors, scales, splines, stats, txdbmaker, utils LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr, GenomeInfoDb, ggbio, biovizBase License: MIT + file LICENSE Archs: x64 Package: OutSplice Version: 1.4.0 Depends: R(>= 4.3) Imports: AnnotationDbi (>= 1.60.0), GenomicRanges (>= 1.49.0), GenomicFeatures (>= 1.50.2), IRanges (>= 2.32.0), org.Hs.eg.db (>= 3.16.0), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.16.0), S4Vectors (>= 0.36.0) Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 Package: OVESEG Version: 1.20.0 Depends: R (>= 3.6) Imports: stats, utils, methods, BiocParallel, SummarizedExperiment, limma, fdrtool, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales License: GPL-2 Archs: x64 Package: PAA Version: 1.38.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.6) Imports: e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR, sva LinkingTo: Rcpp Suggests: BiocStyle, RUnit, BiocGenerics, vsn License: BSD_3_clause + file LICENSE Archs: x64 Package: packFinder Version: 1.16.0 Depends: R (>= 4.1.0) Imports: Biostrings, GenomicRanges, kmer, ape, methods, IRanges, S4Vectors Suggests: biomartr, knitr, rmarkdown, testthat, dendextend, biocViews, BiocCheck, BiocStyle License: GPL-2 Package: padma Version: 1.14.1 Depends: R (>= 4.1.0), SummarizedExperiment, S4Vectors Imports: FactoMineR, MultiAssayExperiment, methods, graphics, stats, utils Suggests: testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA, ggplot2, ggrepel, car, cowplot, reshape2 License: GPL (>= 3) Package: PADOG Version: 1.46.0 Depends: R (>= 3.0.0), KEGGdzPathwaysGEO, methods,Biobase Imports: limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db, hgu133a.db, KEGGREST, nlme Suggests: doParallel, parallel License: GPL (>= 2) Package: pageRank Version: 1.14.0 Depends: R (>= 4.0) Imports: GenomicRanges, igraph, motifmatchr, stats, utils, grDevices, graphics Suggests: bcellViper, BSgenome.Hsapiens.UCSC.hg19, JASPAR2018, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, TFBSTools, GenomicFeatures, annotate License: GPL-2 Package: PAIRADISE Version: 1.20.0 Depends: R (>= 3.6), nloptr Imports: SummarizedExperiment, S4Vectors, stats, methods, abind, BiocParallel Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE Package: paircompviz Version: 1.42.0 Depends: R (>= 2.10), Rgraphviz Imports: Rgraphviz Suggests: multcomp, reshape, rpart, plyr, xtable License: GPL (>= 3.0) Package: pairedGSEA Version: 1.4.0 Depends: R (>= 4.3.0) Imports: DESeq2, DEXSeq, limma, fgsea, sva, SummarizedExperiment, S4Vectors, BiocParallel, ggplot2, aggregation, stats, utils, methods Suggests: writexl, readxl, readr, rhdf5, msigdbr, plotly, testthat (>= 3.0.0), knitr, rmarkdown, covr, BiocStyle License: MIT + file LICENSE Package: pairkat Version: 1.10.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, KEGGREST, igraph, data.table, methods, stats, magrittr, CompQuadForm, tibble Suggests: rmarkdown, knitr, BiocStyle, dplyr License: GPL-3 Package: pandaR Version: 1.36.0 Depends: R (>= 3.0.0), methods, Biobase, BiocGenerics, Imports: matrixStats, igraph, ggplot2, grid, reshape, plyr, RUnit, hexbin Suggests: knitr, rmarkdown License: GPL-2 Package: panelcn.mops Version: 1.26.0 Depends: R (>= 3.5.0), cn.mops, methods, utils, stats, graphics Imports: GenomicRanges, Rsamtools, IRanges, S4Vectors, GenomeInfoDb, grDevices Suggests: knitr, rmarkdown, RUnit, BiocGenerics License: LGPL (>= 2.0) Package: PanomiR Version: 1.8.0 Depends: R (>= 4.2.0) Imports: clusterProfiler, dplyr, forcats, GSEABase, igraph, limma, metap, org.Hs.eg.db, parallel, preprocessCore, RColorBrewer, rlang, tibble, withr, utils Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE Package: panp Version: 1.74.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) Imports: Biobase, methods, stats, utils Suggests: gcrma License: GPL (>= 2) Package: PANR Version: 1.50.0 Depends: R (>= 2.14), igraph Imports: graphics, grDevices, MASS, methods, pvclust, stats, utils, RedeR Suggests: snow License: Artistic-2.0 Package: PanViz Version: 1.6.0 Depends: R (>= 4.2.0) Imports: tidyr, stringr, dplyr, tibble, magrittr, futile.logger, utils, easycsv, rentrez, igraph, RColorBrewer, data.table, colorspace, grDevices, rlang, methods Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, networkD3, License: Artistic-2.0 Package: pareg Version: 1.8.0 Depends: R (>= 4.2), tensorflow (>= 2.2.0), tfprobability (>= 0.10.0) Imports: stats, tidyr, purrr, future, doFuture, foreach, doRNG, tibble, glue, tidygraph, igraph, proxy, dplyr, magrittr, ggplot2, ggraph, rlang, progress, Matrix, keras, nloptr, ggrepel, methods, DOSE, stringr, reticulate, logger, hms, devtools, basilisk Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, plotROC, PRROC, mgsa, topGO, msigdbr, betareg, fgsea, ComplexHeatmap, GGally, ggsignif, circlize, enrichplot, ggnewscale, tidyverse, cowplot, ggfittext, simplifyEnrichment, GSEABenchmarkeR, BiocParallel, ggupset, latex2exp, org.Hs.eg.db, GO.db License: GPL-3 Package: parglms Version: 1.36.0 Depends: methods Imports: BiocGenerics, BatchJobs, foreach, doParallel Suggests: RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges, gwascat, BiocStyle, rmarkdown License: Artistic-2.0 Package: parody Version: 1.62.0 Depends: R (>= 3.5.0), tools, utils Suggests: knitr, BiocStyle, testthat, rmarkdown License: Artistic-2.0 Package: partCNV Version: 1.2.0 Depends: R (>= 3.5.0) Imports: stats, data.table, depmixS4, Seurat, SingleCellExperiment, AnnotationHub, magrittr, GenomicRanges Suggests: BiocStyle, rmarkdown, knitr, IRanges, testthat (>= 3.0.0) License: GPL-2 Package: PAST Version: 1.20.0 Depends: R (>= 4.0) Imports: stats, utils, dplyr, rlang, iterators, parallel, foreach, doParallel, qvalue, rtracklayer, ggplot2, GenomicRanges, S4Vectors Suggests: knitr, rmarkdown License: GPL (>= 3) + file LICENSE Package: Path2PPI Version: 1.34.0 Depends: R (>= 3.2.1), igraph (>= 1.0.1), methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle License: GPL (>= 2) Package: pathifier Version: 1.42.0 Imports: R.oo, princurve (>= 2.0.4) License: Artistic-1.0 Package: pathlinkR Version: 1.0.1 Depends: R (>= 4.3.0) Imports: circlize, clusterProfiler, ComplexHeatmap, dplyr, ggforce, ggplot2, ggpubr, ggraph, ggrepel, grid, igraph, purrr, sigora, stringr, tibble, tidygraph, tidyr, vegan, visNetwork Suggests: AnnotationDbi, BiocStyle, biomaRt, covr, DESeq2, jsonlite, knitr, org.Hs.eg.db, rmarkdown, scales, testthat (>= 3.0.0), vdiffr License: GPL-3 + file LICENSE Package: PathNet Version: 1.44.0 Suggests: PathNetData, RUnit, BiocGenerics License: GPL-3 Package: PathoStat Version: 1.30.0 Depends: R (>= 3.5) Imports: limma, corpcor,matrixStats, reshape2, scales, ggplot2, rentrez, DT, tidyr, plyr, dplyr, phyloseq, shiny, stats, methods, XML, graphics, utils, BiocStyle, edgeR, DESeq2, ComplexHeatmap, plotly, webshot, vegan, shinyjs, glmnet, gmodels, ROCR, RColorBrewer, knitr, devtools, ape Suggests: rmarkdown, testthat License: GPL (>= 2) Package: pathRender Version: 1.72.0 Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods, stats4 Suggests: ALL, hgu95av2.db License: LGPL Package: pathVar Version: 1.34.0 Depends: R (>= 3.3.0), methods, ggplot2, gridExtra Imports: EMT, mclust, Matching, data.table, stats, grDevices, graphics, utils License: LGPL (>= 2.0) Package: pathview Version: 1.44.0 Depends: R (>= 3.5.0) Imports: KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, org.Hs.eg.db, KEGGREST, methods, utils Suggests: gage, org.Mm.eg.db, org.EcK12.eg.db, RUnit, BiocGenerics License: GPL (>= 3.0) Package: pathwayPCA Version: 1.20.0 Depends: R (>= 3.1) Imports: lars, methods, parallel, stats, survival, utils Suggests: airway, circlize, grDevices, knitr, RCurl, reshape2, rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse License: GPL-3 Package: pcaExplorer Version: 2.30.0 Imports: DESeq2, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, genefilter, ggplot2 (>= 2.0.0), heatmaply, plotly, scales, NMF, plyr, topGO, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, ggrepel, DT, shinyAce, threejs, biomaRt, pheatmap, knitr, rmarkdown, base64enc, tidyr, grDevices, methods Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, htmltools License: MIT + file LICENSE Package: pcaMethods Version: 1.96.0 Depends: Biobase, methods Imports: BiocGenerics, Rcpp (>= 0.11.3), MASS LinkingTo: Rcpp Suggests: matrixStats, lattice, ggplot2 License: GPL (>= 3) Archs: x64 Package: PCAN Version: 1.32.0 Depends: R (>= 3.3), BiocParallel Imports: grDevices, stats Suggests: BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb License: CC BY-NC-ND 4.0 Package: PCAtools Version: 2.16.0 Depends: ggplot2, ggrepel Imports: lattice, grDevices, cowplot, methods, reshape2, stats, Matrix, DelayedMatrixStats, DelayedArray, BiocSingular, BiocParallel, Rcpp, dqrng LinkingTo: Rcpp, beachmat, BH, dqrng Suggests: testthat, scran, BiocGenerics, knitr, Biobase, GEOquery, hgu133a.db, ggplotify, beachmat, RMTstat, ggalt, DESeq2, airway, org.Hs.eg.db, magrittr, rmarkdown License: GPL-3 Archs: x64 Package: pcxn Version: 2.26.0 Depends: R (>= 3.4), pcxnData Imports: methods, grDevices, utils, pheatmap Suggests: igraph, annotate, org.Hs.eg.db License: MIT + file LICENSE Package: PDATK Version: 1.12.0 Depends: R (>= 4.1), SummarizedExperiment Imports: data.table, MultiAssayExperiment, ConsensusClusterPlus, igraph, ggplotify, matrixStats, RColorBrewer, clusterRepro, CoreGx, caret, survminer, methods, S4Vectors, BiocGenerics, survival, stats, plyr, dplyr, MatrixGenerics, BiocParallel, rlang, piano, scales, survcomp, genefu, ggplot2, switchBox, reportROC, pROC, verification, utils Suggests: testthat (>= 3.0.0), msigdbr, BiocStyle, rmarkdown, knitr, HDF5Array License: MIT + file LICENSE Package: pdInfoBuilder Version: 1.68.0 Depends: R (>= 3.2.0), methods, Biobase (>= 2.27.3), RSQLite (>= 1.0.0), affxparser (>= 1.39.4), oligo (>= 1.31.5) Imports: Biostrings (>= 2.35.12), BiocGenerics (>= 0.13.11), DBI (>= 0.3.1), IRanges (>= 2.1.43), oligoClasses (>= 1.29.6), S4Vectors (>= 0.5.22) License: Artistic-2.0 Archs: x64 Package: PeacoQC Version: 1.14.0 Depends: R (>= 4.0) Imports: circlize, ComplexHeatmap, flowCore, flowWorkspace, ggplot2, grDevices, grid, gridExtra, methods, plyr, stats, utils Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 3) Package: peakPantheR Version: 1.18.0 Depends: R (>= 4.2) Imports: foreach (>= 1.4.4), doParallel (>= 1.0.11), ggplot2 (>= 3.5.0), gridExtra (>= 2.3), MSnbase (>= 2.4.0), mzR (>= 2.12.0), stringr (>= 1.2.0), methods (>= 3.4.0), XML (>= 3.98.1.10), minpack.lm (>= 1.2.1), scales(>= 0.5.0), shiny (>= 1.0.5), bslib, shinycssloaders (>= 1.0.0), DT (>= 0.15), pracma (>= 2.2.3), utils, lubridate, svglite (>= 2.1.1) Suggests: testthat, devtools, faahKO, msdata, knitr, rmarkdown, pander, BiocStyle License: GPL-3 Package: PECA Version: 1.40.0 Depends: R (>= 3.3) Imports: ROTS, limma, affy, genefilter, preprocessCore, aroma.affymetrix, aroma.core Suggests: SpikeIn License: GPL (>= 2) Package: peco Version: 1.16.0 Depends: R (>= 3.5.0) Imports: assertthat, circular, conicfit, doParallel, foreach, genlasso (>= 1.4), graphics, methods, parallel, scater, SingleCellExperiment, SummarizedExperiment, stats, utils Suggests: knitr, rmarkdown License: GPL (>= 3) Package: Pedixplorer Version: 1.0.0 Depends: R (>= 4.3.0) Imports: graphics, stats, methods, ggplot2, utils, grDevices, stringr, plyr, dplyr, tidyr, quadprog, Matrix, S4Vectors, testthat Suggests: diffviewer, vdiffr, rmarkdown, BiocStyle, knitr, withr, magick License: Artistic-2.0 Package: pengls Version: 1.10.0 Depends: R (>= 4.2.0) Imports: glmnet, nlme, stats, BiocParallel Suggests: knitr,rmarkdown,testthat License: GPL-2 Package: PepsNMR Version: 1.22.0 Depends: R (>= 3.6) Imports: Matrix, ptw, ggplot2, gridExtra, matrixStats, reshape2, methods, graphics, stats Suggests: knitr, markdown, rmarkdown, BiocStyle, PepsNMRData License: GPL-2 | file LICENSE Package: pepStat Version: 1.38.0 Depends: R (>= 3.0.0), Biobase, IRanges Imports: limma, fields, GenomicRanges, ggplot2, plyr, tools, methods, data.table Suggests: pepDat, Pviz, knitr, shiny License: Artistic-2.0 Package: pepXMLTab Version: 1.38.0 Depends: R (>= 3.0.1) Imports: XML(>= 3.98-1.1) Suggests: RUnit, BiocGenerics License: Artistic-2.0 Package: PERFect Version: 1.18.0 Depends: R (>= 3.6.0), sn (>= 1.5.2) Imports: ggplot2 (>= 3.0.0), phyloseq (>= 1.28.0), zoo (>= 1.8.3), psych (>= 1.8.4), stats (>= 3.6.0), Matrix (>= 1.2.14), fitdistrplus (>= 1.0.12), parallel (>= 3.6.0) Suggests: knitr, rmarkdown, kableExtra, ggpubr License: Artistic-2.0 Package: periodicDNA Version: 1.14.0 Depends: R (>= 4.0), Biostrings, GenomicRanges, IRanges, BSgenome, BiocParallel Imports: S4Vectors, rtracklayer, stats, GenomeInfoDb, magrittr, zoo, ggplot2, methods, parallel, cowplot Suggests: BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, reticulate, testthat, covr, knitr, rmarkdown, pkgdown License: GPL-3 + file LICENSE Package: pfamAnalyzeR Version: 1.4.0 Depends: R (>= 4.3.0), readr, stringr, dplyr Imports: utils, tibble, magrittr Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE Package: pgca Version: 1.28.0 Imports: utils, stats Suggests: knitr, testthat, rmarkdown License: GPL (>= 2) Package: pgxRpi Version: 1.0.3 Depends: R (>= 4.2) Imports: utils, methods, grDevices, graphics, circlize, httr, dplyr, attempt, lubridate, survival, survminer, ggplot2, plyr, GenomicRanges, SummarizedExperiment, S4Vectors, parallelly Suggests: BiocStyle, rmarkdown, knitr, testthat License: Artistic-2.0 Package: phantasusLite Version: 1.2.0 Depends: R (>= 4.2) Imports: data.table, rhdf5client(>= 1.25.1), httr, stringr, stats, utils, Biobase, methods Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rhdf5, GEOquery License: MIT + file LICENSE Package: PharmacoGx Version: 3.8.0 Depends: R (>= 3.6), CoreGx Imports: BiocGenerics, Biobase, S4Vectors, SummarizedExperiment, MultiAssayExperiment, BiocParallel, ggplot2, RColorBrewer, magicaxis, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table, checkmate, boot, coop LinkingTo: Rcpp Suggests: pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown, BiocStyle, R.utils License: GPL (>= 3) Archs: x64 Package: PhenoGeneRanker Version: 1.12.0 Imports: igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel Suggests: knitr, rmarkdown License: Creative Commons Attribution 4.0 International License Package: phenomis Version: 1.6.0 Depends: SummarizedExperiment Imports: Biobase, biodb, biodbChebi, data.table, futile.logger, ggplot2, ggrepel, graphics, grDevices, grid, htmlwidgets, igraph, limma, methods, MultiAssayExperiment, MultiDataSet, PMCMRplus, plotly, ranger, RColorBrewer, ropls, stats, tibble, tidyr, utils, VennDiagram Suggests: BiocGenerics, BiocStyle, biosigner, CLL, knitr, omicade4, rmarkdown, testthat License: CeCILL Package: phenopath Version: 1.28.0 Imports: Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr, tibble, ggplot2, tidyr LinkingTo: Rcpp Suggests: knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment License: Apache License (== 2.0) Archs: x64 Package: phenoTest Version: 1.52.0 Depends: R (>= 3.6.0), Biobase, methods, annotate, Heatplus, BMA, ggplot2, Hmisc Imports: survival, limma, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, hgu133a.db, ellipse Suggests: GSEABase, GO.db Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db License: GPL (>= 2) Package: PhenStat Version: 2.40.0 Depends: R (>= 3.5.0) Imports: SmoothWin, methods, car, nlme, nortest, MASS, msgps, logistf, knitr, tools, pingr, ggplot2, reshape, corrplot, graph, lme4, graphics, grDevices, utils, stats Suggests: RUnit, BiocGenerics License: file LICENSE Package: philr Version: 1.30.0 Imports: ape, phangorn, tidyr, ggplot2, ggtree, methods Suggests: testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia License: GPL-3 Package: PhIPData Version: 1.12.0 Depends: R (>= 4.1.0), SummarizedExperiment (>= 1.3.81) Imports: BiocFileCache, BiocGenerics, methods, GenomicRanges, IRanges, S4Vectors, edgeR, cli, utils Suggests: BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr, withr License: MIT + file LICENSE Package: phosphonormalizer Version: 1.28.0 Depends: R (>= 4.0) Imports: plyr, stats, graphics, matrixStats, methods Suggests: knitr, rmarkdown, testthat Enhances: MSnbase License: GPL (>= 2) Package: PhosR Version: 1.14.0 Depends: R (>= 4.2.0) Imports: ruv, e1071, dendextend, limma, pcaMethods, stats, RColorBrewer, circlize, dplyr, igraph, pheatmap, preprocessCore, tidyr, rlang, graphics, grDevices, utils, SummarizedExperiment, methods, S4Vectors, BiocGenerics, ggplot2, GGally, ggdendro, ggpubr, network, reshape2, ggtext, stringi Suggests: testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown, org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle, stringr, calibrate License: GPL-3 + file LICENSE Package: PhyloProfile Version: 1.18.0 Depends: R (>= 4.3.0) Imports: ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table, DT, energy, ExperimentHub, ggplot2, gridExtra, pbapply, RColorBrewer, RCurl, shiny, shinyBS, shinycssloaders, shinyFiles, shinyjs, stringr, OmaDB, plyr, xml2, zoo, yaml Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE Package: phyloseq Version: 1.48.0 Depends: R (>= 3.3.0) Imports: ade4 (>= 1.7-4), ape (>= 5.0), Biobase (>= 2.36.2), BiocGenerics (>= 0.22.0), biomformat (>= 1.0.0), Biostrings (>= 2.40.0), cluster (>= 2.0.4), data.table (>= 1.10.4), foreach (>= 1.4.3), ggplot2 (>= 2.1.0), igraph (>= 1.0.1), methods (>= 3.3.0), multtest (>= 2.28.0), plyr (>= 1.8.3), reshape2 (>= 1.4.1), scales (>= 0.4.0), vegan (>= 2.5) Suggests: BiocStyle (>= 2.4), DESeq2 (>= 1.16.1), genefilter (>= 1.58), knitr (>= 1.16), magrittr (>= 1.5), metagenomeSeq (>= 1.14), rmarkdown (>= 1.6), testthat (>= 1.0.2) Enhances: doParallel (>= 1.0.10) License: AGPL-3 Package: piano Version: 2.20.0 Depends: R (>= 3.5) Imports: BiocGenerics, Biobase, gplots, igraph, relations, marray, fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard, visNetwork, scales, grDevices, graphics, stats, utils, methods Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle License: GPL (>= 2) Package: pickgene Version: 1.76.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) Package: PICS Version: 2.48.0 Depends: R (>= 3.0.0) Imports: utils, stats, graphics, grDevices, methods, IRanges, GenomicRanges, Rsamtools, GenomicAlignments Suggests: rtracklayer, parallel, knitr License: Artistic-2.0 Archs: x64 Package: Pigengene Version: 1.30.0 Depends: R (>= 4.0.3), graph, BiocStyle (>= 2.28.0) Imports: bnlearn (>= 4.7), C50 (>= 0.1.2), MASS, matrixStats, partykit, Rgraphviz, WGCNA, GO.db, impute, preprocessCore, grDevices, graphics, stats, utils, parallel, pheatmap (>= 1.0.8), dplyr, gdata, clusterProfiler, ReactomePA, ggplot2, openxlsx, DBI, DOSE Suggests: org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), biomaRt (>= 2.30.0), knitr, AnnotationDbi, energy License: GPL (>= 2) Package: PING Version: 2.48.0 Depends: R(>= 3.5.0) Imports: methods, PICS, graphics, grDevices, stats, Gviz, fda, BSgenome, stats4, BiocGenerics, IRanges, GenomicRanges, S4Vectors Suggests: parallel, ShortRead, rtracklayer License: Artistic-2.0 Archs: x64 Package: pipeComp Version: 1.14.0 Depends: R (>= 4.1) Imports: BiocParallel, S4Vectors, ComplexHeatmap, SingleCellExperiment, SummarizedExperiment, Seurat, matrixStats, Matrix, cluster, aricode, methods, utils, dplyr, grid, scales, scran, viridisLite, clue, randomcoloR, ggplot2, cowplot, intrinsicDimension, scater, knitr, reshape2, stats, Rtsne, uwot, circlize, RColorBrewer Suggests: BiocStyle, rmarkdown License: GPL Package: pipeFrame Version: 1.20.0 Depends: R (>= 4.0.0), Imports: BSgenome, digest, visNetwork, magrittr, methods, Biostrings, GenomeInfoDb, parallel, stats, utils, rmarkdown Suggests: BiocManager, knitr, rtracklayer, testthat, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 Package: PIPETS Version: 1.0.1 Depends: R (>= 4.4.0) Imports: dplyr, utils, stats, GenomicRanges, BiocGenerics, methods Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 Package: PIUMA Version: 1.0.0 Depends: R (>= 4.3), ggplot2 Imports: cluster, umap, tsne, kernlab, vegan, dbscan, igraph, scales, Hmisc, patchwork, grDevices, stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, testthat, rmarkdown License: GPL-3 + file LICENSE Package: planet Version: 1.12.0 Depends: R (>= 4.3) Imports: methods, tibble, magrittr, dplyr Suggests: ggplot2, testthat, tidyr, scales, minfi, EpiDISH, knitr, rmarkdown License: GPL-2 Package: planttfhunter Version: 1.4.0 Depends: R (>= 4.2.0) Imports: Biostrings, SummarizedExperiment, utils, methods Suggests: BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 Package: plasmut Version: 1.2.0 Depends: R (>= 4.3.0) Imports: tibble, stats, dplyr Suggests: knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf, BiocStyle, biocViews, testthat (>= 3.0.0) License: Artistic-2.0 Package: plgem Version: 1.76.0 Depends: R (>= 2.10) Imports: utils, Biobase (>= 2.5.5), MASS, methods License: GPL-2 Package: plier Version: 1.74.0 Depends: R (>= 2.0), methods Imports: affy, Biobase, methods License: GPL (>= 2) Archs: x64 Package: PloGO2 Version: 1.16.0 Depends: R (>= 4.0), GO.db, GOstats Imports: lattice, httr, openxlsx, xtable License: GPL-2 Package: plotgardener Version: 1.10.2 Depends: R (>= 4.1.0) Imports: curl, data.table, dplyr, GenomeInfoDb, GenomicRanges, grDevices, grid, ggplotify, IRanges, methods, plyranges, purrr, Rcpp, RColorBrewer, rlang, stats, strawr, tools, utils, withr LinkingTo: Rcpp Suggests: AnnotationDbi, AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures, ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, pdftools, png, rmarkdown, scales, showtext, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene License: MIT + file LICENSE Archs: x64 Package: PLPE Version: 1.64.0 Depends: R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods License: GPL (>= 2) Package: PLSDAbatch Version: 1.0.0 Depends: R (>= 4.3.0) Imports: mixOmics, scales, Rdpack, ggplot2, gridExtra, ggpubr, lmerTest, performance, grid, stats, pheatmap, vegan, Biobase, BiocStyle, TreeSummarizedExperiment Suggests: knitr, rmarkdown, testthat, badger License: GPL-3 Package: plyinteractions Version: 1.2.0 Depends: R (>= 4.3.0) Imports: InteractionSet, GenomeInfoDb, BiocGenerics, GenomicRanges, plyranges, IRanges, S4Vectors, rlang, dplyr, tibble, tidyselect, methods, utils Suggests: tidyverse, BSgenome.Mmusculus.UCSC.mm10, Biostrings, BiocParallel, scales, HiContactsData, rtracklayer, BiocStyle, covr, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), RefManageR License: Artistic-2.0 Package: plyranges Version: 1.24.0 Depends: R (>= 3.5), BiocGenerics, IRanges (>= 2.12.0), GenomicRanges (>= 1.28.4) Imports: methods, dplyr, rlang (>= 0.2.0), magrittr, tidyselect (>= 1.0.0), rtracklayer, GenomicAlignments, GenomeInfoDb, Rsamtools, S4Vectors (>= 0.23.10), utils Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 2.1.0), HelloRanges, HelloRangesData, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, covr, ggplot2 License: Artistic-2.0 Package: pmm Version: 1.36.0 Depends: R (>= 2.10) Imports: lme4, splines License: GPL-3 Package: pmp Version: 1.16.0 Depends: R (>= 4.0) Imports: stats, impute, pcaMethods, missForest, ggplot2, methods, SummarizedExperiment, S4Vectors, matrixStats, grDevices, reshape2, utils Suggests: testthat, covr, knitr, rmarkdown, BiocStyle, gridExtra, magick License: GPL-3 Package: PoDCall Version: 1.12.0 Depends: R (>= 4.4) Imports: ggplot2, gridExtra, mclust, diptest, rlist, shiny, DT, LaplacesDemon, purrr, shinyjs, readr, grDevices, stats, utils Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 Package: podkat Version: 1.36.0 Depends: R (>= 3.5.0), methods, Rsamtools (>= 1.99.1), GenomicRanges Imports: Rcpp (>= 0.11.1), parallel, stats (>= 4.3.0), graphics, grDevices, utils, Biobase, BiocGenerics, Matrix, GenomeInfoDb, IRanges, Biostrings, BSgenome (>= 1.32.0) LinkingTo: Rcpp, Rhtslib (>= 1.15.3) Suggests: BSgenome.Hsapiens.UCSC.hg38.masked, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24), VariantAnnotation, SummarizedExperiment, knitr License: GPL (>= 2) Archs: x64 Package: pogos Version: 1.24.0 Depends: R (>= 3.5.0), rjson (>= 0.2.15), httr (>= 1.3.1) Imports: methods, S4Vectors, utils, shiny, ontoProc, ggplot2, graphics Suggests: knitr, DT, ontologyPlot, testthat, rmarkdown, BiocStyle License: Artistic-2.0 Package: polyester Version: 1.39.0 Depends: R (>= 3.0.0) Imports: Biostrings (>= 2.32.0), IRanges, S4Vectors, logspline, limma, zlibbioc Suggests: knitr, ballgown, markdown License: Artistic-2.0 Package: POMA Version: 1.14.0 Depends: R (>= 4.0) Imports: broom, caret, ComplexHeatmap, dbscan, dplyr, DESeq2, FSA, ggplot2, ggrepel, glmnet, impute, janitor, limma, lme4, magrittr, MASS, mixOmics, randomForest, RankProd (>= 3.14), rlang, SummarizedExperiment, sva, tibble, tidyr, utils, uwot, vegan Suggests: BiocStyle, covr, ggraph, ggtext, knitr, patchwork, plotly, tidyverse, testthat (>= 2.3.2) License: GPL-3 Package: powerTCR Version: 1.24.0 Imports: cubature, doParallel, evmix, foreach, magrittr, methods, parallel, purrr, stats, truncdist, vegan, VGAM Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: Artistic-2.0 Package: POWSC Version: 1.12.0 Depends: R (>= 4.1), Biobase, SingleCellExperiment, MAST Imports: pheatmap, ggplot2, RColorBrewer, grDevices, SummarizedExperiment, limma Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-2 Package: ppcseq Version: 1.12.0 Depends: R (>= 4.1.0), rstan (>= 2.18.1) Imports: benchmarkme, dplyr, edgeR, foreach, ggplot2, graphics, lifecycle, magrittr, methods, parallel, purrr, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rlang, rstantools (>= 2.1.1), stats, tibble, tidybayes, tidyr (>= 0.8.3.9000), utils LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: knitr, testthat, BiocStyle, rmarkdown License: GPL-3 Archs: x64 Package: PPInfer Version: 1.30.0 Depends: biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb, yeastExpData Imports: httr, grDevices, graphics, stats, utils License: Artistic-2.0 Package: pqsfinder Version: 2.20.0 Depends: R (>= 3.5.0), Biostrings Imports: Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods LinkingTo: Rcpp, BH (>= 1.78.0) Suggests: BiocStyle, knitr, rmarkdown, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi License: BSD_2_clause + file LICENSE Archs: x64 Package: pram Version: 1.20.0 Depends: R (>= 3.6) Imports: methods, BiocParallel, tools, utils, data.table (>= 1.11.8), GenomicAlignments (>= 1.16.0), rtracklayer (>= 1.40.6), BiocGenerics (>= 0.26.0), GenomeInfoDb (>= 1.16.0), GenomicRanges (>= 1.32.0), IRanges (>= 2.14.12), Rsamtools (>= 1.32.3), S4Vectors (>= 0.18.3) Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL (>= 3) Package: prebs Version: 1.44.0 Depends: R (>= 2.14.0), GenomicAlignments, affy, RPA Imports: parallel, methods, stats, GenomicRanges (>= 1.13.3), IRanges, Biobase, GenomeInfoDb, S4Vectors Suggests: prebsdata, hgu133plus2cdf, hgu133plus2probe License: Artistic-2.0 Package: preciseTAD Version: 1.14.0 Depends: R (>= 4.1) Imports: S4Vectors, IRanges, GenomicRanges, randomForest, ModelMetrics, e1071, PRROC, pROC, caret, utils, cluster, dbscan, doSNOW, foreach, pbapply, stats, parallel, gtools, rCGH Suggests: knitr, rmarkdown, testthat, BiocCheck, BiocManager, BiocStyle License: MIT + file LICENSE Package: PREDA Version: 1.50.0 Depends: R (>= 2.9.0), Biobase, lokern (>= 1.0.9), multtest, stats, methods, annotate Suggests: quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata Enhances: Rmpi, rsprng License: GPL-2 Package: preprocessCore Version: 1.66.0 Imports: stats License: LGPL (>= 2) Archs: x64 Package: primirTSS Version: 1.22.0 Depends: R (>= 3.5.0) Imports: GenomicRanges (>= 1.32.2), S4Vectors (>= 0.18.2), rtracklayer (>= 1.40.3), dplyr (>= 0.7.6), stringr (>= 1.3.1), tidyr (>= 0.8.1), Biostrings (>= 2.48.0), purrr (>= 0.2.5), BSgenome.Hsapiens.UCSC.hg38 (>= 1.4.1), phastCons100way.UCSC.hg38 (>= 3.7.1), GenomicScores (>= 1.4.1), shiny (>= 1.0.5), Gviz (>= 1.24.0), BiocGenerics (>= 0.26.0), IRanges (>= 2.14.10), TFBSTools (>= 1.18.0), JASPAR2018 (>= 1.1.1), tibble (>= 1.4.2), R.utils (>= 2.6.0), stats, utils Suggests: knitr, rmarkdown License: GPL-2 Package: PrInCE Version: 1.20.0 Depends: R (>= 3.6.0) Imports: purrr (>= 0.2.4), dplyr (>= 0.7.4), tidyr (>= 0.8.99), forecast (>= 8.2), progress (>= 1.1.2), Hmisc (>= 4.0), naivebayes (>= 0.9.1), robustbase (>= 0.92-7), ranger (>= 0.8.0), LiblineaR (>= 2.10-8), speedglm (>= 0.3-2), tester (>= 0.1.7), magrittr (>= 1.5), Biobase (>= 2.40.0), MSnbase (>= 2.8.3), stats, utils, methods, Rdpack (>= 0.7) Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 + file LICENSE Package: proActiv Version: 1.14.0 Depends: R (>= 4.0.0) Imports: AnnotationDbi, BiocParallel, data.table, dplyr, DESeq2, IRanges, GenomicRanges, GenomicFeatures, GenomicAlignments, GenomeInfoDb, ggplot2, gplots, graphics, methods, rlang, scales, S4Vectors, SummarizedExperiment, stats, tibble, txdbmaker Suggests: testthat, rmarkdown, knitr, Rtsne, gridExtra License: MIT + file LICENSE Package: proBAMr Version: 1.38.0 Depends: R (>= 3.0.1), IRanges, AnnotationDbi Imports: GenomicRanges, Biostrings, GenomicFeatures, txdbmaker, rtracklayer Suggests: RUnit, BiocGenerics License: Artistic-2.0 Package: PROcess Version: 1.80.0 Depends: Icens Imports: graphics, grDevices, Icens, stats, utils License: Artistic-2.0 Package: procoil Version: 2.32.0 Depends: R (>= 3.3.0), kebabs Imports: methods, stats, graphics, S4Vectors, Biostrings, utils Suggests: knitr License: GPL (>= 2) Package: proDA Version: 1.18.0 Imports: stats, utils, methods, BiocGenerics, SummarizedExperiment, S4Vectors, extraDistr Suggests: testthat (>= 2.1.0), MSnbase, dplyr, stringr, readr, tidyr, tibble, limma, DEP, numDeriv, pheatmap, knitr, rmarkdown, BiocStyle License: GPL-3 Package: profileplyr Version: 1.20.0 Depends: R (>= 3.6), BiocGenerics, SummarizedExperiment Imports: GenomicRanges, stats, soGGi, methods, utils, S4Vectors, R.utils, dplyr, magrittr, tidyr, IRanges, rjson, ChIPseeker,GenomicFeatures,TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene,org.Hs.eg.db,org.Mm.eg.db,rGREAT, pheatmap, ggplot2, EnrichedHeatmap, ComplexHeatmap, grid, circlize, BiocParallel, rtracklayer, GenomeInfoDb, grDevices, rlang, tiff, Rsamtools Suggests: BiocStyle, testthat, knitr, rmarkdown, png, Cairo License: GPL (>= 3) Package: profileScoreDist Version: 1.32.0 Depends: R(>= 3.3) Imports: Rcpp, BiocGenerics, methods, graphics LinkingTo: Rcpp Suggests: BiocStyle, knitr, MotifDb License: MIT + file LICENSE Archs: x64 Package: progeny Version: 1.26.0 Depends: R (>= 3.6.0) Imports: Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra, decoupleR, reshape2 Suggests: airway, biomaRt, BiocFileCache, broom, Seurat, SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl, pheatmap, tibble, rmarkdown, testthat (>= 2.1.0) License: Apache License (== 2.0) | file LICENSE Package: projectR Version: 1.20.0 Depends: R (>= 4.0.0) Imports: methods, cluster, stats, limma, NMF, ROCR, ggalluvial, RColorBrewer, dplyr, fgsea, reshape2, viridis, scales, Matrix, MatrixModels, msigdbr, ggplot2, cowplot, ggrepel, umap, tsne Suggests: BiocStyle, CoGAPS, gridExtra, grid, testthat, devtools, knitr, rmarkdown, ComplexHeatmap, gplots, SeuratObject License: GPL (== 2) Package: pRoloc Version: 1.44.1 Depends: R (>= 3.5), MSnbase (>= 1.19.20), MLInterfaces (>= 1.67.10), methods, Rcpp (>= 0.10.3), BiocParallel Imports: stats4, Biobase, mclust (>= 4.3), caret, e1071, sampling, class, kernlab, lattice, nnet, randomForest, proxy, FNN, hexbin, BiocGenerics, stats, dendextend, RColorBrewer, scales, MASS, knitr, mvtnorm, LaplacesDemon, coda, mixtools, gtools, plyr, ggplot2, biomaRt, utils, grDevices, graphics LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.41.0), dplyr, akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape, magick License: GPL-2 Archs: x64 Package: pRolocGUI Version: 2.14.0 Depends: methods, R (>= 3.1.0), pRoloc (>= 1.27.6), Biobase, MSnbase (>= 2.1.11) Imports: shiny (>= 0.9.1), scales, dplyr, DT (>= 0.1.40), graphics, utils, ggplot2, shinydashboardPlus (>= 2.0.0), colourpicker, shinyhelper, shinyWidgets, shinyjs, colorspace, stats, grDevices, grid, BiocGenerics, shinydashboard Suggests: pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown, testthat (>= 3.0.0) License: GPL-2 Package: PROMISE Version: 1.56.0 Depends: R (>= 3.1.0), Biobase, GSEABase Imports: Biobase, GSEABase, stats License: GPL (>= 2) Package: PROPER Version: 1.36.0 Depends: R (>= 3.3) Imports: edgeR Suggests: BiocStyle,DESeq2,DSS,knitr License: GPL Package: PROPS Version: 1.26.0 Imports: bnlearn, reshape2, sva, stats, utils, Biobase Suggests: knitr, rmarkdown License: GPL-2 Package: Prostar Version: 1.36.2 Depends: R (>= 4.4.0) Imports: DAPAR (>= 1.36.2), DAPARdata (>= 1.34.0), rhandsontable, data.table, shiny, shinyBS, shinyAce, highcharter, htmlwidgets, webshot, shinythemes, later, shinycssloaders, future, promises, shinyjqui, tibble, ggplot2, gplots, shinyjs, vioplot, Biobase, DT, R.utils, RColorBrewer, XML, colourpicker, gtools, markdown, rclipboard, sass, shinyTree, shinyWidgets Suggests: BiocStyle, BiocManager, testthat, knitr License: Artistic-2.0 Package: proteasy Version: 1.6.0 Depends: R (>= 4.2.0) Imports: data.table, stringr, ensembldb, AnnotationFilter, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, EnsDb.Rnorvegicus.v79, Rcpi, methods, utils Suggests: BiocStyle, knitr, rmarkdown, igraph, ComplexHeatmap, viridis, License: GPL-3 Package: proteinProfiles Version: 1.44.0 Depends: R (>= 2.15.2) Imports: graphics, stats Suggests: testthat License: GPL-3 Package: ProteoDisco Version: 1.10.0 Depends: R (>= 4.1.0), Imports: BiocGenerics (>= 0.38.0), BiocParallel (>= 1.26.0), Biostrings (>= 2.60.1), checkmate (>= 2.0.0), cleaver (>= 1.30.0), dplyr (>= 1.0.6), GenomeInfoDb (>= 1.28.0), GenomicFeatures (>= 1.44.0), GenomicRanges (>= 1.44.0), IRanges (>= 2.26.0), methods (>= 4.1.0), ParallelLogger (>= 2.0.1), plyr (>= 1.8.6), rlang (>= 0.4.11), S4Vectors (>= 0.30.0), tibble (>= 3.1.2), tidyr (>= 1.1.3), VariantAnnotation (>= 1.36.0), XVector (>= 0.32.0), Suggests: AnnotationDbi (>= 1.54.1), BSgenome (>= 1.60.0), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.3), BiocStyle (>= 2.20.1), DelayedArray (>= 0.18.0), devtools (>= 2.4.2), knitr (>= 1.33), matrixStats (>= 0.59.0), markdown (>= 1.1), org.Hs.eg.db (>= 3.13.0), purrr (>= 0.3.4), RCurl (>= 1.98.1.3), readr (>= 1.4.0), ggplot2 (>= 3.3.5), rmarkdown (>= 2.9), rtracklayer (>= 1.52.0), seqinr (>= 4.2.8), stringr (>= 1.4.0), reshape2 (>= 1.4.4), scales (>= 1.1.1), testthat (>= 3.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2) License: GPL-3 Package: ProteoMM Version: 1.22.0 Depends: R (>= 3.5) Imports: gdata, biomaRt, ggplot2, ggrepel, gtools, stats, matrixStats, graphics Suggests: BiocStyle, knitr, rmarkdown License: MIT Package: protGear Version: 1.8.0 Depends: R (>= 4.2), dplyr (>= 0.8.0) , limma (>= 3.40.2) ,vsn (>= 3.54.0) Imports: magrittr (>= 1.5) , stats (>= 3.6) , ggplot2 (>= 3.3.0) , tidyr (>= 1.1.3) , data.table (>= 1.14.0), ggpubr (>= 0.4.0), gtools (>= 3.8.2) , tibble (>= 3.1.0) , rmarkdown (>= 2.9) , knitr (>= 1.33), utils (>= 3.6), genefilter (>= 1.74.0), readr (>= 2.0.1) , Biobase (>= 2.52.0), plyr (>= 1.8.6) , Kendall (>= 2.2) , shiny (>= 1.0.0) , purrr (>= 0.3.4), plotly (>= 4.9.0) , MASS (>= 7.3) , htmltools (>= 0.4.0) , flexdashboard (>= 0.5.2) , shinydashboard (>= 0.7.1) , GGally (>= 2.1.2) , pheatmap (>= 1.0.12) , grid(>= 4.1.1), styler (>= 1.6.1) , factoextra (>= 1.0.7) ,FactoMineR (>= 2.4) , rlang (>= 0.4.11), remotes (>= 2.4.0) Suggests: gridExtra (>= 2.3), png (>= 0.1-7) , magick (>= 2.7.3) , ggplotify (>= 0.1.0) , scales (>= 1.1.1) , shinythemes (>= 1.2.0) , shinyjs (>= 2.0.0) , shinyWidgets (>= 0.6.2) , shinycssloaders (>= 1.0.0) , shinyalert (>= 3.0.0) , shinyFiles (>= 0.9.1) , shinyFeedback (>= 0.3.0) License: GPL-3 Package: ProtGenerics Version: 1.36.0 Depends: methods Suggests: testthat License: Artistic-2.0 Package: PSEA Version: 1.38.0 Imports: Biobase, MASS Suggests: BiocStyle License: Artistic-2.0 Package: psichomics Version: 1.30.0 Depends: R (>= 4.0), shiny (>= 1.7.0), shinyBS Imports: AnnotationDbi, AnnotationHub, BiocFileCache, cluster, colourpicker, data.table, digest, dplyr, DT (>= 0.2), edgeR, fastICA, fastmatch, ggplot2, ggrepel, graphics, grDevices, highcharter (>= 0.5.0), htmltools, httr, jsonlite, limma, pairsD3, plyr, purrr, Rcpp (>= 0.12.14), recount, Rfast, R.utils, reshape2, shinyjs, stringr, stats, SummarizedExperiment, survival, tools, utils, XML, xtable, methods LinkingTo: Rcpp Suggests: testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi, spelling License: MIT + file LICENSE Archs: x64 Package: PSMatch Version: 1.8.0 Depends: S4Vectors Imports: utils, stats, igraph, methods, Matrix, BiocParallel, BiocGenerics, ProtGenerics (>= 1.27.1), QFeatures, MsCoreUtils Suggests: msdata, rpx, mzID, mzR, Spectra, SummarizedExperiment, BiocStyle, rmarkdown, knitr, factoextra, testthat License: Artistic-2.0 Package: psygenet2r Version: 1.36.0 Depends: R (>= 3.4) Imports: stringr, RCurl, igraph, ggplot2, reshape2, grid, parallel, biomaRt, BgeeDB, topGO, Biobase, labeling, GO.db Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE Package: ptairMS Version: 1.12.0 Imports: Biobase, bit64, chron, data.table, doParallel, DT, enviPat, foreach, ggplot2, graphics, grDevices, ggpubr, gridExtra, Hmisc, methods, minpack.lm, MSnbase, parallel, plotly, rhdf5, rlang, Rcpp, shiny, shinyscreenshot, signal, scales, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), ptairData, ropls License: GPL-3 Archs: x64 Package: puma Version: 3.46.0 Depends: R (>= 3.2.0), oligo (>= 1.32.0),graphics,grDevices, methods, stats, utils, mclust, oligoClasses Imports: Biobase (>= 2.5.5), affy (>= 1.46.0), affyio, oligoClasses Suggests: pumadata, affydata, snow, limma, ROCR,annotate License: LGPL Archs: x64 Package: PureCN Version: 2.10.0 Depends: R (>= 3.5.0), DNAcopy, VariantAnnotation (>= 1.14.1) Imports: GenomicRanges (>= 1.20.3), IRanges (>= 2.2.1), RColorBrewer, S4Vectors, data.table, grDevices, graphics, stats, utils, SummarizedExperiment, GenomeInfoDb, GenomicFeatures, Rsamtools, Biobase, Biostrings, BiocGenerics, rtracklayer, ggplot2, gridExtra, futile.logger, VGAM, tools, methods, mclust, rhdf5, Matrix Suggests: BiocParallel, BiocStyle, PSCBS, R.utils, TxDb.Hsapiens.UCSC.hg19.knownGene, covr, knitr, optparse, org.Hs.eg.db, jsonlite, markdown, rmarkdown, testthat Enhances: genomicsdb (>= 0.0.3) License: Artistic-2.0 Package: pvac Version: 1.52.0 Depends: R (>= 2.8.0) Imports: affy (>= 1.20.0), stats, Biobase Suggests: pbapply, affydata, ALLMLL, genefilter License: LGPL (>= 2.0) Package: pvca Version: 1.44.0 Depends: R (>= 2.15.1) Imports: Matrix, Biobase, vsn, stats, lme4 Suggests: golubEsets License: LGPL (>= 2.0) Package: Pviz Version: 1.38.0 Depends: R(>= 3.0.0), Gviz(>= 1.7.10) Imports: biovizBase, Biostrings, GenomicRanges, IRanges, data.table, methods Suggests: knitr, pepDat License: Artistic-2.0 Package: pwalign Version: 1.0.0 Depends: BiocGenerics, S4Vectors, IRanges, Biostrings (>= 2.71.5) Imports: methods, utils LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: RUnit Enhances: Rmpi License: Artistic-2.0 Archs: x64 Package: PWMEnrich Version: 4.40.0 Depends: R (>= 3.5.0), methods, BiocGenerics, Biostrings Imports: grid, seqLogo, gdata, evd, S4Vectors Suggests: MotifDb, BSgenome, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background, BiocStyle, knitr License: LGPL (>= 2) Package: pwOmics Version: 1.36.0 Depends: R (>= 3.2) Imports: data.table, rBiopaxParser, igraph, STRINGdb, graphics, gplots, Biobase, BiocGenerics, AnnotationDbi, biomaRt, AnnotationHub, GenomicRanges, graph, grDevices, stats, utils Suggests: ebdbNet, longitudinal, Mfuzz, RUnit License: GPL (>= 2) Package: qcmetrics Version: 1.42.0 Depends: R (>= 3.3) Imports: Biobase, methods, knitr, tools, xtable, pander, S4Vectors Suggests: affy, MSnbase, ggplot2, lattice, mzR, BiocStyle, rmarkdown, markdown License: GPL-2 Package: QDNAseq Version: 1.40.0 Depends: R (>= 3.1.0) Imports: graphics, methods, stats, utils, Biobase (>= 2.18.0), CGHbase (>= 1.18.0), CGHcall (>= 2.18.0), DNAcopy (>= 1.32.0), GenomicRanges (>= 1.20), IRanges (>= 2.2), matrixStats (>= 0.60.0), R.utils (>= 2.9.0), Rsamtools (>= 1.20), future.apply (>= 1.8.1) Suggests: BiocStyle (>= 1.8.0), BSgenome (>= 1.38.0), digest (>= 0.6.20), GenomeInfoDb (>= 1.6.0), future (>= 1.22.1), parallelly (>= 1.28.1), R.cache (>= 0.13.0), QDNAseq.hg19, QDNAseq.mm10 License: GPL Package: QFeatures Version: 1.14.2 Depends: R (>= 4.0), MultiAssayExperiment Imports: methods, stats, utils, S4Vectors, IRanges, SummarizedExperiment, BiocGenerics, ProtGenerics (>= 1.35.1), AnnotationFilter, lazyeval, Biobase, MsCoreUtils (>= 1.7.2), igraph, grDevices, plotly, tidyr, tidyselect, reshape2 Suggests: SingleCellExperiment, MsDataHub (>= 1.3.3), Matrix, HDF5Array, msdata, ggplot2, gplots, dplyr, limma, DT, shiny, shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute, norm, ComplexHeatmap License: Artistic-2.0 Package: qmtools Version: 1.8.0 Depends: R (>= 4.2.0), SummarizedExperiment Imports: rlang, ggplot2, patchwork, heatmaply, methods, MsCoreUtils, stats, igraph, VIM, scales, grDevices, graphics, limma Suggests: Rtsne, missForest, vsn, pcaMethods, pls, MsFeatures, impute, imputeLCMD, nlme, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: GPL-3 Package: qpcrNorm Version: 1.62.0 Depends: methods, Biobase, limma, affy License: LGPL (>= 2) Package: qpgraph Version: 2.38.0 Depends: R (>= 3.5) Imports: methods, parallel, Matrix (>= 1.5-0), grid, annotate, graph (>= 1.45.1), Biobase, S4Vectors, BiocParallel, AnnotationDbi, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, mvtnorm, qtl, Rgraphviz Suggests: RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db, rlecuyer, snow, Category, GOstats License: GPL (>= 2) Archs: x64 Package: qPLEXanalyzer Version: 1.22.0 Depends: R (>= 4.0), Biobase, MSnbase Imports: assertthat, BiocGenerics, Biostrings, dplyr (>= 1.0.0), ggdendro, ggplot2, graphics, grDevices, IRanges, limma, magrittr, preprocessCore, purrr, RColorBrewer, readr, rlang, scales, stats, stringr, tibble, tidyr, tidyselect, utils Suggests: gridExtra, knitr, qPLEXdata, rmarkdown, statmod, testthat, UniProt.ws, vdiffr License: GPL-2 Package: qsea Version: 1.30.0 Depends: R (>= 4.3) Imports: Biostrings, graphics, gtools, methods, stats, utils, HMMcopy, rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges, limma, GenomeInfoDb, BiocGenerics, grDevices, zoo, BiocParallel, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown, BiocManager, MASS License: GPL-2 Archs: x64 Package: qsmooth Version: 1.20.0 Depends: R (>= 4.0) Imports: SummarizedExperiment, utils, sva, stats, methods, graphics, Hmisc Suggests: bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat License: GPL-3 Package: QSutils Version: 1.22.0 Depends: R (>= 3.5), Biostrings, pwalign, BiocGenerics, methods Imports: ape, stats, psych Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: GPL-2 Package: qsvaR Version: 1.8.0 Depends: R (>= 4.2), SummarizedExperiment Imports: sva, stats, ggplot2, methods Suggests: BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: Artistic-2.0 Package: QTLExperiment Version: 1.2.0 Depends: SummarizedExperiment Imports: methods, rlang, checkmate, dplyr, collapse, vroom, tidyr, tibble, utils, stats, ashr, S4Vectors, BiocGenerics Suggests: testthat, BiocStyle, knitr, rmarkdown, covr License: GPL-3 Package: Qtlizer Version: 1.18.0 Depends: R (>= 3.6.0) Imports: httr, curl, GenomicRanges, stringi Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 Package: quantiseqr Version: 1.12.0 Depends: R (>= 4.1.0) Imports: Biobase, limSolve, MASS, methods, preprocessCore, stats, SummarizedExperiment, ggplot2, tidyr, rlang, utils Suggests: AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery, knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat, tibble License: GPL-3 Package: quantro Version: 1.38.0 Depends: R (>= 4.0) Imports: Biobase, minfi, doParallel, foreach, iterators, ggplot2, methods, RColorBrewer Suggests: rmarkdown, knitr, RUnit, BiocGenerics, BiocStyle License: GPL-3 Package: quantsmooth Version: 1.70.0 Depends: R(>= 2.10.0), quantreg, grid License: GPL-2 Package: QuartPAC Version: 1.36.0 Depends: iPAC, GraphPAC, SpacePAC, data.table Imports: Biostrings, pwalign Suggests: RUnit, BiocGenerics, rgl License: GPL-2 Package: QuasR Version: 1.44.0 Depends: R (>= 4.4), parallel, GenomicRanges, Rbowtie Imports: methods, grDevices, graphics, utils, stats, tools, BiocGenerics, S4Vectors, IRanges, Biobase, Biostrings, BSgenome, Rsamtools (>= 2.13.1), GenomicFeatures, txdbmaker, ShortRead, BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles, AnnotationDbi LinkingTo: Rhtslib (>= 1.99.1) Suggests: Gviz, BiocStyle, GenomicAlignments, Rhisat2, knitr, rmarkdown, covr, testthat License: GPL-2 Archs: x64 Package: QuaternaryProd Version: 1.38.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.3), dplyr, yaml (>= 2.1.18) LinkingTo: Rcpp Suggests: knitr License: GPL (>= 3) Archs: x64 Package: QUBIC Version: 1.32.0 Depends: R (>= 3.1), biclust Imports: Rcpp (>= 0.11.0), methods, Matrix LinkingTo: Rcpp, RcppArmadillo Suggests: QUBICdata, qgraph, fields, knitr, rmarkdown Enhances: RColorBrewer License: CC BY-NC-ND 4.0 + file LICENSE Archs: x64 Package: qusage Version: 2.38.0 Depends: R (>= 2.10), limma (>= 3.14), methods Imports: utils, Biobase, nlme, emmeans, fftw License: GPL (>= 2) Package: qvalue Version: 2.36.0 Depends: R(>= 2.10) Imports: splines, ggplot2, grid, reshape2 Suggests: knitr License: LGPL Package: R3CPET Version: 1.36.0 Depends: R (>= 3.2), Rcpp (>= 0.10.4), methods Imports: methods, parallel, ggplot2, pheatmap, clValid, igraph, data.table, reshape2, Hmisc, RCurl, BiocGenerics, S4Vectors, IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8), ggbio LinkingTo: Rcpp Suggests: BiocStyle, knitr, TxDb.Hsapiens.UCSC.hg19.knownGene, biovizBase, biomaRt, AnnotationDbi, org.Hs.eg.db, shiny, ChIPpeakAnno License: GPL (>= 2) Archs: x64 Package: r3Cseq Version: 1.50.0 Depends: GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue Imports: methods, GenomeInfoDb, IRanges, Biostrings, data.table, sqldf, RColorBrewer Suggests: BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Rnorvegicus.UCSC.rn5.masked License: GPL-3 Package: R453Plus1Toolbox Version: 1.54.0 Depends: R (>= 2.12.0), methods, VariantAnnotation (>= 1.25.11), Biostrings (>= 2.47.6), pwalign, Biobase Imports: utils, grDevices, graphics, stats, tools, xtable, R2HTML, TeachingDemos, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector, GenomicRanges (>= 1.31.8), SummarizedExperiment, biomaRt, BSgenome (>= 1.47.3), Rsamtools, ShortRead (>= 1.37.1) Suggests: rtracklayer, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2 License: LGPL-3 Archs: x64 Package: R4RNA Version: 1.32.0 Depends: R (>= 3.2.0), Biostrings (>= 2.38.0) License: GPL-3 Package: RadioGx Version: 2.8.0 Depends: R (>= 4.1), CoreGx Imports: SummarizedExperiment, BiocGenerics, data.table, S4Vectors, Biobase, parallel, BiocParallel, RColorBrewer, caTools, magicaxis, methods, reshape2, scales, grDevices, graphics, stats, utils, assertthat, matrixStats, downloader Suggests: rmarkdown, BiocStyle, knitr, pander, markdown License: GPL-3 Package: raer Version: 1.2.0 Imports: stats, methods, GenomicRanges, IRanges, Rsamtools, BSgenome, Biostrings, SummarizedExperiment, SingleCellExperiment, S4Vectors, GenomeInfoDb, GenomicAlignments, GenomicFeatures, BiocGenerics, BiocParallel, rtracklayer, Matrix, cli LinkingTo: Rhtslib Suggests: testthat (>= 3.0.0), knitr, DESeq2, edgeR, limma, rmarkdown, BiocStyle, ComplexHeatmap, TxDb.Hsapiens.UCSC.hg38.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, BSgenome.Hsapiens.NCBI.GRCh38, scater, scran, scuttle, AnnotationHub, covr, raerdata, txdbmaker License: MIT + file LICENSE Archs: x64 Package: RaggedExperiment Version: 1.28.0 Depends: R (>= 4.2.0), GenomicRanges (>= 1.37.17) Imports: BiocBaseUtils, BiocGenerics, GenomeInfoDb, IRanges, Matrix, MatrixGenerics, methods, S4Vectors, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, MultiAssayExperiment License: Artistic-2.0 Package: RAIDS Version: 1.2.0 Depends: R (>= 4.2.0), gdsfmt, SNPRelate, stats, utils, GENESIS Imports: S4Vectors, GenomicRanges, ensembldb, BSgenome, AnnotationDbi, methods, class, pROC, IRanges, AnnotationFilter, rlang, VariantAnnotation, MatrixGenerics, Suggests: testthat, knitr, rmarkdown, BiocStyle, withr, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 License: Apache License (>= 2) Package: rain Version: 1.38.0 Depends: R (>= 2.10), gmp, multtest Suggests: lattice, BiocStyle License: GPL-2 Package: ramr Version: 1.12.0 Depends: R (>= 4.1), GenomicRanges, parallel, doParallel, foreach, doRNG, methods Imports: IRanges, BiocGenerics, ggplot2, reshape2, EnvStats, ExtDist, matrixStats, S4Vectors Suggests: RUnit, knitr, rmarkdown, gridExtra, annotatr, LOLA, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 Package: ramwas Version: 1.28.0 Depends: R (>= 3.3.0), methods, filematrix Imports: graphics, stats, utils, digest, glmnet, KernSmooth, grDevices, GenomicAlignments, Rsamtools, parallel, biomaRt, Biostrings, BiocGenerics Suggests: knitr, rmarkdown, pander, BiocStyle, BSgenome.Ecoli.NCBI.20080805 License: LGPL-3 Archs: x64 Package: randPack Version: 1.50.0 Depends: methods Imports: Biobase License: Artistic-2.0 Package: randRotation Version: 1.16.0 Imports: methods, graphics, utils, stats, Rdpack (>= 0.7) Suggests: knitr, BiocParallel, lme4, nlme, rmarkdown, BiocStyle, testthat (>= 2.1.0), limma, sva License: GPL-3 Package: RankProd Version: 3.30.0 Depends: R (>= 3.2.1), stats, methods, Rmpfr, gmp Imports: graphics License: file LICENSE License_restricts_use: yes Package: RAREsim Version: 1.8.0 Depends: R (>= 4.1.0) Imports: nloptr Suggests: markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-3 Package: RareVariantVis Version: 2.32.0 Depends: BiocGenerics, VariantAnnotation, googleVis, GenomicFeatures Imports: S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, gtools, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, SummarizedExperiment, GenomicScores Suggests: knitr License: Artistic-2.0 Package: Rarr Version: 1.4.0 Imports: jsonlite, httr, stringr, R.utils, utils, paws.storage, methods Suggests: BiocStyle, covr, knitr, tinytest, mockery License: MIT + file LICENSE Archs: x64 Package: rawDiag Version: 1.0.0 Depends: R (>= 4.3) Imports: dplyr, ggplot2 (>= 3.4), grDevices, hexbin, htmltools, BiocManager, BiocParallel, rawrr (>= 1.10), rlang, reshape2, scales, shiny (>= 1.5), stats, utils Suggests: BiocStyle (>= 2.28), ExperimentHub, tartare, knitr, testthat License: GPL-3 Package: rawrr Version: 1.12.0 Depends: R (>= 4.1) Imports: grDevices, graphics, stats, utils Suggests: BiocStyle (>= 2.5), ExperimentHub, knitr, protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat License: GPL-3 Package: RbcBook1 Version: 1.72.0 Depends: R (>= 2.10), Biobase, graph, rpart License: Artistic-2.0 Package: Rbec Version: 1.12.0 Imports: Rcpp (>= 1.0.6), dada2, ggplot2, readr, doParallel, foreach, grDevices, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: LGPL-3 Archs: x64 Package: RBGL Version: 1.80.0 Depends: graph, methods Imports: methods LinkingTo: BH Suggests: Rgraphviz, XML, RUnit, BiocGenerics, BiocStyle, knitr License: Artistic-2.0 Archs: x64 Package: RBioFormats Version: 1.4.0 Imports: EBImage, methods, rJava (>= 0.9-6), S4Vectors, stats Suggests: BiocStyle, knitr, testthat, xml2 License: GPL-3 Package: RBioinf Version: 1.64.0 Depends: graph, methods Suggests: Rgraphviz License: Artistic-2.0 Archs: x64 Package: rBiopaxParser Version: 2.44.0 Depends: R (>= 4.0), data.table Imports: XML Suggests: Rgraphviz, RCurl, graph, RUnit, BiocGenerics, RBGL, igraph License: GPL (>= 2) Package: rBLAST Version: 1.0.0 Depends: Biostrings (>= 2.26.2) Imports: methods, utils, BiocFileCache Suggests: knitr, rmarkdown, testthat License: GPL-3 Package: RBM Version: 1.36.0 Depends: R (>= 3.2.0), limma, marray License: GPL (>= 2) Package: Rbowtie Version: 1.44.0 Imports: utils Suggests: testthat, parallel, BiocStyle, knitr, rmarkdown License: Artistic-2.0 | file LICENSE Archs: x64 Package: rbsurv Version: 2.62.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), survival License: GPL (>= 2) Package: RCAS Version: 1.30.0 Depends: R (>= 3.5.0), plotly (>= 4.5.2), DT (>= 0.2), data.table Imports: GenomicRanges, IRanges, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomeInfoDb (>= 1.12.0), Biostrings, rtracklayer, GenomicFeatures, txdbmaker, rmarkdown (>= 0.9.5), genomation (>= 1.5.5), knitr (>= 1.12.3), BiocGenerics, S4Vectors, plotrix, pbapply, RSQLite, proxy, pheatmap, ggplot2, cowplot, seqLogo, utils, ranger, gprofiler2 Suggests: testthat, covr, BiocManager License: Artistic-2.0 Package: RCASPAR Version: 1.50.0 License: GPL (>= 3) Package: rcellminer Version: 2.26.0 Depends: R (>= 3.2), Biobase, rcellminerData (>= 2.0.0) Imports: stringr, gplots, ggplot2, methods, stats, utils, shiny Suggests: knitr, RColorBrewer, sqldf, BiocGenerics, testthat, BiocStyle, jsonlite, heatmaply, glmnet, foreach, doSNOW, parallel, rmarkdown License: LGPL-3 + file LICENSE Package: rCGH Version: 1.34.0 Depends: R (>= 3.4),methods,stats,utils,graphics Imports: plyr,DNAcopy,lattice,ggplot2,grid,shiny (>= 0.11.1), limma,affy,mclust,TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db,GenomicFeatures,GenomeInfoDb,GenomicRanges,AnnotationDbi, parallel,IRanges,grDevices,aCGH Suggests: BiocStyle, knitr, BiocGenerics, RUnit License: Artistic-2.0 Package: RcisTarget Version: 1.24.0 Depends: R (>= 3.5.0) Imports: AUCell (>= 1.1.6), BiocGenerics, data.table, graphics, GenomeInfoDb, GenomicRanges, arrow (>= 2.0.0), dplyr, tibble, GSEABase, methods, R.utils, stats, SummarizedExperiment, S4Vectors, utils, zoo Suggests: Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach, gplots, rtracklayer, igraph, knitr, RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat, visNetwork Enhances: doMC, doRNG License: GPL-3 Package: RCM Version: 1.20.0 Depends: R (>= 4.0), DBI Imports: RColorBrewer, alabama, edgeR, reshape2, tseries, stats, VGAM, ggplot2 (>= 2.2.1.9000), nleqslv, phyloseq, tensor, MASS, grDevices, graphics, methods Suggests: knitr, rmarkdown, testthat License: GPL-2 Package: Rcpi Version: 1.40.0 Depends: R (>= 3.0.2) Imports: Biostrings, GOSemSim, RCurl, doParallel, foreach, methods, pwalign, rjson, rlang, stats, utils Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 | file LICENSE Package: RCSL Version: 1.12.0 Depends: R (>= 4.1) Imports: RcppAnnoy, igraph, NbClust, Rtsne, ggplot2(>= 3.4.0), methods, pracma, umap, grDevices, graphics, stats, Rcpp (>= 0.11.0), MatrixGenerics, SingleCellExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown, mclust, tidyverse, tinytex License: Artistic-2.0 Package: RCX Version: 1.8.0 Depends: R (>= 4.2.0) Imports: jsonlite, plyr, igraph, methods Suggests: BiocStyle, testthat, knitr, rmarkdown, base64enc, graph License: MIT + file LICENSE Package: RCy3 Version: 2.24.0 Imports: httr, methods, RJSONIO, XML, utils, BiocGenerics, stats, graph, fs, uuid, stringi, glue, RCurl, base64url, base64enc, IRkernel, IRdisplay, RColorBrewer, gplots Suggests: BiocStyle, knitr, rmarkdown, igraph, grDevices License: MIT + file LICENSE Package: RCyjs Version: 2.26.1 Depends: R (>= 3.5.0), BrowserViz (>= 2.7.18), graph (>= 1.56.0) Imports: methods, httpuv (>= 1.5.0), BiocGenerics, base64enc, utils Suggests: RUnit, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE Package: rDGIdb Version: 1.30.0 Imports: jsonlite,httr,methods,graphics Suggests: BiocStyle,knitr,testthat License: MIT + file LICENSE Package: Rdisop Version: 1.64.0 Depends: R (>= 2.0.0), Rcpp LinkingTo: Rcpp Suggests: RUnit License: GPL-2 Archs: x64 Package: RDRToolbox Version: 1.54.0 Depends: R (>= 2.9.0) Imports: graphics, grDevices, methods, stats, MASS, rgl Suggests: golubEsets License: GPL (>= 2) Package: ReactomeContentService4R Version: 1.12.0 Imports: httr, jsonlite, utils, magick (>= 2.5.1), data.table, doParallel, foreach, parallel Suggests: pdftools, testthat, knitr, rmarkdown License: Apache License (>= 2.0) | file LICENSE Package: ReactomeGraph4R Version: 1.12.0 Depends: R (>= 4.1) Imports: neo4r, utils, getPass, jsonlite, purrr, magrittr, data.table, rlang, ReactomeContentService4R, doParallel, parallel, foreach Suggests: knitr, rmarkdown, testthat, stringr, networkD3, visNetwork, wesanderson License: Apache License (>= 2) Package: ReactomeGSA Version: 1.18.0 Imports: jsonlite, httr, progress, ggplot2, methods, gplots, RColorBrewer, dplyr, tidyr, Biobase Suggests: testthat, knitr, rmarkdown, ReactomeGSA.data, devtools Enhances: limma, edgeR, Seurat (>= 3.0), scater License: MIT + file LICENSE Package: ReactomePA Version: 1.48.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, DOSE (>= 3.5.1), enrichplot, ggplot2 (>= 3.3.5), ggraph, reactome.db, igraph, graphite, gson Suggests: BiocStyle, clusterProfiler, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat License: GPL-2 Package: ReadqPCR Version: 1.50.0 Depends: R(>= 2.14.0), Biobase, methods Suggests: qpcR License: LGPL-3 Package: REBET Version: 1.22.0 Depends: ASSET Imports: stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 Archs: x64 Package: rebook Version: 1.14.0 Imports: utils, methods, knitr (>= 1.32), rmarkdown, CodeDepends, dir.expiry, filelock, BiocStyle Suggests: testthat, igraph, XML, BiocManager, RCurl, bookdown, rappdirs, yaml, BiocParallel, OSCA.intro, OSCA.workflows License: GPL-3 Package: receptLoss Version: 1.16.0 Depends: R (>= 3.6.0) Imports: dplyr, ggplot2, magrittr, tidyr, SummarizedExperiment Suggests: knitr, rmarkdown, testthat (>= 2.1.0), here License: GPL-3 + file LICENSE Package: reconsi Version: 1.16.0 Imports: phyloseq, ks, reshape2, ggplot2, stats, methods, graphics, grDevices, matrixStats, Matrix Suggests: knitr, rmarkdown, testthat License: GPL-2 Package: recount Version: 1.30.2 Depends: R (>= 3.5.0), SummarizedExperiment Imports: BiocParallel, derfinder, downloader, GEOquery, GenomeInfoDb, GenomicRanges, IRanges, methods, RCurl, rentrez, rtracklayer (>= 1.35.3), S4Vectors, stats, utils Suggests: AnnotationDbi, BiocManager, BiocStyle (>= 2.5.19), DESeq2, sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures, txdbmaker, knitr (>= 1.6), org.Hs.eg.db, RefManageR, regionReport (>= 1.9.4), rmarkdown (>= 0.9.5), testthat (>= 2.1.0), covr, pheatmap, DT, edgeR, ggplot2, RColorBrewer License: Artistic-2.0 Package: recount3 Version: 1.14.0 Depends: SummarizedExperiment Imports: BiocFileCache, methods, rtracklayer, S4Vectors, utils, httr, data.table, R.utils, Matrix, GenomicRanges, sessioninfo, tools Suggests: BiocStyle, covr, knitcitations, knitr, RefManageR, rmarkdown, testthat, pryr, interactiveDisplayBase, recount License: Artistic-2.0 Package: recountmethylation Version: 1.14.0 Depends: R (>= 4.1) Imports: minfi, HDF5Array, rhdf5, S4Vectors, utils, methods, RCurl, R.utils, BiocFileCache, basilisk, reticulate, DelayedMatrixStats Suggests: minfiData, minfiDataEPIC, knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub License: Artistic-2.0 Package: recoup Version: 1.32.0 Depends: R (>= 4.0.0), GenomicRanges, GenomicAlignments, ggplot2, ComplexHeatmap Imports: BiocGenerics, biomaRt, Biostrings, circlize, GenomeInfoDb, GenomicFeatures, graphics, grDevices, httr, IRanges, methods, parallel, RSQLite, Rsamtools, rtracklayer, S4Vectors, stats, stringr, txdbmaker, utils Suggests: grid, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager, BSgenome, RMySQL License: GPL (>= 3) Package: RedeR Version: 3.0.0 Depends: R (>= 4.0), methods Imports: scales, igraph Suggests: knitr, rmarkdown, markdown, BiocStyle, TreeAndLeaf License: GPL-3 Package: RedisParam Version: 1.6.0 Depends: R (>= 4.2.0), BiocParallel (>= 1.29.12) Imports: methods, redux, withr, futile.logger Suggests: rmarkdown, knitr, testthat, BiocStyle License: Artistic-2.0 Package: REDseq Version: 1.50.0 Depends: R (>= 3.5.0), BiocGenerics, BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome, ChIPpeakAnno Imports: AnnotationDbi, graphics, IRanges (>= 1.13.5), stats, utils License: GPL (>= 2) Package: RefPlus Version: 1.74.0 Depends: R (>= 2.8.0), Biobase (>= 2.1.0), affy (>= 1.20.0), affyPLM (>= 1.18.0), preprocessCore (>= 1.4.0) Suggests: affydata License: GPL (>= 2) Package: RegEnrich Version: 1.14.0 Depends: R (>= 4.0.0), S4Vectors, dplyr, tibble, BiocSet, SummarizedExperiment Imports: randomForest, fgsea, DOSE, BiocParallel, DESeq2, limma, WGCNA, ggplot2 (>= 2.2.0), methods, reshape2, magrittr, BiocStyle Suggests: GEOquery, rmarkdown, knitr, BiocManager, testthat License: GPL (>= 2) Package: regionalpcs Version: 1.2.0 Depends: R (>= 4.3.0) Imports: dplyr, PCAtools, tibble, GenomicRanges Suggests: knitr, rmarkdown, RMTstat, testthat (>= 3.0.0), BiocStyle, tidyr, minfiData, TxDb.Hsapiens.UCSC.hg19.knownGene, IRanges License: MIT + file LICENSE Package: RegionalST Version: 1.2.0 Depends: R (>= 4.3.0) Imports: stats, grDevices, utils, ggplot2, dplyr, scater, gridExtra, BayesSpace, fgsea, magrittr, SingleCellExperiment, RColorBrewer, Seurat, S4Vectors, tibble, TOAST, assertthat, colorspace, shiny, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, gplots, testthat (>= 3.0.0) License: GPL-3 Package: regioneR Version: 1.36.0 Depends: GenomicRanges Imports: memoise, GenomicRanges, IRanges, BSgenome, Biostrings, rtracklayer, parallel, graphics, stats, utils, methods, GenomeInfoDb, S4Vectors, tools Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19.masked, testthat License: Artistic-2.0 Package: regioneReloaded Version: 1.6.0 Depends: R (>= 4.2), regioneR Imports: stats, RColorBrewer, Rtsne, umap, ggplot2, ggrepel, reshape2, methods, scales, cluster, grid, grDevices Suggests: rmarkdown, BiocStyle, GenomeInfoDb, knitr, testthat (>= 3.0.0) License: Artistic-2.0 Package: regionReport Version: 1.38.0 Depends: R(>= 3.2) Imports: BiocStyle (>= 2.5.19), derfinder (>= 1.25.3), DEFormats, DESeq2, GenomeInfoDb, GenomicRanges, knitr (>= 1.6), knitrBootstrap (>= 0.9.0), methods, RefManageR, rmarkdown (>= 0.9.5), S4Vectors, SummarizedExperiment, utils Suggests: BiocManager, biovizBase, bumphunter (>= 1.7.6), derfinderPlot (>= 1.29.1), sessioninfo, DT, edgeR, ggbio (>= 1.35.2), ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker License: Artistic-2.0 Package: regsplice Version: 1.30.0 Imports: glmnet, SummarizedExperiment, S4Vectors, limma, edgeR, stats, pbapply, utils, methods Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE Package: regutools Version: 1.16.0 Depends: R (>= 4.0) Imports: AnnotationDbi, AnnotationHub, Biostrings, DBI, GenomicRanges, Gviz, IRanges, RCy3, RSQLite, S4Vectors, methods, stats, utils, BiocFileCache Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 2.1.0), covr License: Artistic-2.0 Package: REMP Version: 1.28.0 Depends: R (>= 3.6), SummarizedExperiment(>= 1.1.6), minfi (>= 1.22.0) Imports: readr, rtracklayer, graphics, stats, utils, methods, settings, BiocGenerics, S4Vectors, Biostrings, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel, doParallel, parallel, foreach, caret, kernlab, ranger, BSgenome, AnnotationHub, org.Hs.eg.db, impute, iterators Suggests: IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, minfiDataEPIC License: GPL-3 Package: Repitools Version: 1.50.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.8.0) Imports: parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, BSgenome (>= 1.47.3), gplots, grid, MASS, gsmoothr, edgeR (>= 3.4.0), DNAcopy, Rsolnp, cluster Suggests: ShortRead, BSgenome.Hsapiens.UCSC.hg18 License: LGPL (>= 2) Archs: x64 Package: ReportingTools Version: 2.44.0 Depends: methods, knitr, utils Imports: Biobase,hwriter,Category,GOstats,limma(>= 3.17.5),lattice,AnnotationDbi,edgeR, annotate,PFAM.db, GSEABase, BiocGenerics(>= 0.1.6), grid, XML, R.utils, DESeq2(>= 1.3.41), ggplot2, ggbio, IRanges Suggests: RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla, org.Sc.sgd.db, rmarkdown, markdown License: Artistic-2.0 Package: RepViz Version: 1.20.0 Depends: R (>= 3.5.1), GenomicRanges (>= 1.30.0), Rsamtools (>= 1.34.1), IRanges (>= 2.14.0), biomaRt (>= 2.36.0), S4Vectors (>= 0.18.0), graphics, grDevices, utils Suggests: rmarkdown, knitr, testthat License: GPL-3 Package: ResidualMatrix Version: 1.14.1 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular License: GPL-3 Package: RESOLVE Version: 1.6.0 Depends: R (>= 4.1.0) Imports: Biostrings, BSgenome, BSgenome.Hsapiens.1000genomes.hs37d5, data.table, GenomeInfoDb, GenomicRanges, glmnet, ggplot2, gridExtra, IRanges, lsa, MutationalPatterns, nnls, parallel, reshape2, S4Vectors Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE Package: retrofit Version: 1.4.0 Depends: R (>= 4.2), Rcpp LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, testthat, DescTools, ggplot2, corrplot, cowplot, grid, colorspace, png, reshape2, pals, RCurl License: GPL-3 Archs: x64 Package: rexposome Version: 1.26.0 Depends: R (>= 3.5), Biobase Imports: methods, utils, stats, lsr, FactoMineR, stringr, circlize, corrplot, ggplot2, ggridges, reshape2, pryr, S4Vectors, imputeLCMD, scatterplot3d, glmnet, gridExtra, grid, Hmisc, gplots, gtools, scales, lme4, grDevices, graphics, ggrepel, mice Suggests: mclust, flexmix, testthat, BiocStyle, knitr, formatR, rmarkdown License: MIT + file LICENSE Package: rfaRm Version: 1.16.0 Imports: httr, stringi, rsvg, magick, data.table, Biostrings, utils, rvest, xml2, IRanges, S4Vectors, jsonlite Suggests: R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics, RUnit License: GPL-3 Package: Rfastp Version: 1.14.0 Imports: Rcpp, rjson, ggplot2, reshape2 LinkingTo: Rcpp, Rhtslib, zlibbioc Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 + file LICENSE Archs: x64 Package: rfPred Version: 1.42.0 Depends: R (>= 3.5.0), methods Imports: utils, GenomeInfoDb, data.table, IRanges, GenomicRanges, parallel, Rsamtools Suggests: BiocStyle License: GPL (>= 2) Archs: x64 Package: rGADEM Version: 2.52.0 Depends: R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo Imports: Biostrings, GenomicRanges, methods, graphics, seqLogo Suggests: BSgenome.Hsapiens.UCSC.hg19, rtracklayer License: Artistic-2.0 Archs: x64 Package: rGenomeTracks Version: 1.10.0 Depends: R (>= 4.1.0), Imports: imager, reticulate, methods, rGenomeTracksData Suggests: rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-3 Package: RgnTX Version: 1.6.0 Depends: R (>= 4.2.0) Imports: GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, graphics, IRanges, methods, regioneR, S4Vectors, stats, TxDb.Hsapiens.UCSC.hg19.knownGene Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) License: Artistic-2.0 Package: rgoslin Version: 1.8.0 Imports: Rcpp (>= 1.0.3), dplyr LinkingTo: Rcpp Suggests: testthat (>= 2.1.0), BiocStyle, knitr, rmarkdown, kableExtra, BiocManager, stringr, stringi, ggplot2, tibble, lipidr License: MIT + file LICENSE Archs: x64 Package: RGraph2js Version: 1.32.0 Imports: utils, whisker, rjson, digest, graph Suggests: RUnit, BiocStyle, BiocGenerics, xtable, sna License: GPL-2 Package: Rgraphviz Version: 2.48.0 Depends: R (>= 2.6.0), methods, utils, graph, grid Imports: stats4, graphics, grDevices Suggests: RUnit, BiocGenerics, XML License: EPL Archs: x64 Package: rGREAT Version: 2.6.0 Depends: R (>= 4.0.0), GenomicRanges, IRanges, methods Imports: graphics, rjson, GetoptLong (>= 0.0.9), RCurl, utils, stats, GlobalOptions, shiny, DT, GenomicFeatures, digest, GO.db, progress, circlize, AnnotationDbi, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, RColorBrewer, S4Vectors, GenomeInfoDb, foreach, doParallel, Rcpp LinkingTo: Rcpp Suggests: testthat (>= 0.3), knitr, rmarkdown, BiocManager, org.Mm.eg.db, msigdbr, KEGGREST, reactome.db Enhances: BioMartGOGeneSets, UniProtKeywords License: MIT + file LICENSE Archs: x64 Package: RGSEA Version: 1.38.0 Depends: R(>= 2.10.0) Imports: BiocGenerics Suggests: BiocStyle, GEOquery, knitr, RUnit License: GPL (>= 3) Package: rgsepd Version: 1.36.0 Depends: R (>= 4.2.0), DESeq2, goseq (>= 1.28) Imports: gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment, AnnotationDbi Suggests: boot, tools, BiocGenerics, knitr, xtable License: GPL-3 Package: rhdf5 Version: 2.48.0 Depends: R (>= 4.0.0), methods Imports: Rhdf5lib (>= 1.13.4), rhdf5filters (>= 1.15.5) LinkingTo: Rhdf5lib Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr, ggplot2, mockery, BiocParallel License: Artistic-2.0 Archs: x64 Package: rhdf5client Version: 1.26.0 Depends: R (>= 3.6), methods, DelayedArray Imports: httr, rjson, utils, data.table Suggests: knitr, testthat, BiocStyle, DT, rmarkdown License: Artistic-2.0 Archs: x64 Package: rhdf5filters Version: 1.16.0 LinkingTo: Rhdf5lib Suggests: BiocStyle, knitr, rmarkdown, tinytest, rhdf5 (>= 2.47.7) License: BSD_2_clause + file LICENSE Archs: x64 Package: Rhdf5lib Version: 1.26.0 Depends: R (>= 4.2.0) Suggests: BiocStyle, knitr, rmarkdown, tinytest, mockery License: Artistic-2.0 Archs: x64 Package: Rhisat2 Version: 1.20.0 Depends: R (>= 4.4.0) Imports: txdbmaker, SGSeq, GenomicRanges, methods, utils Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 Archs: x64 Package: Rhtslib Version: 3.0.0 Imports: tools, zlibbioc LinkingTo: zlibbioc Suggests: knitr, rmarkdown, BiocStyle License: LGPL (>= 2) Archs: x64 Package: RiboCrypt Version: 1.10.0 Depends: R (>= 3.6.0), ORFik (>= 1.13.12) Imports: bslib, BiocGenerics, BiocParallel, Biostrings, data.table, dplyr, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, httr, IRanges, jsonlite, knitr, markdown, NGLVieweR, plotly, rlang, RCurl, shiny, shinycssloaders, shinyhelper, shinyjqui, stringr Suggests: testthat, rmarkdown, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE Package: RiboDiPA Version: 1.12.0 Depends: R (>= 4.1), Rsamtools, GenomicFeatures, GenomicAlignments Imports: Rcpp (>= 1.0.2), graphics, stats, data.table, elitism, methods, S4Vectors, IRanges, GenomicRanges, matrixStats, reldist, doParallel, foreach, parallel, qvalue, DESeq2, ggplot2, BiocFileCache, BiocGenerics, txdbmaker LinkingTo: Rcpp Suggests: knitr, rmarkdown License: LGPL (>= 3) Archs: x64 Package: RiboProfiling Version: 1.34.0 Depends: R (>= 3.5.0), Biostrings Imports: BiocGenerics, GenomeInfoDb, GenomicRanges, IRanges, reshape2, GenomicFeatures, grid, plyr, S4Vectors, GenomicAlignments, ggplot2, ggbio, Rsamtools, rtracklayer, data.table, sqldf Suggests: knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment License: GPL-3 Package: ribor Version: 1.16.0 Depends: R (>= 3.6.0) Imports: dplyr, ggplot2, hash, methods, rhdf5, rlang, stats, S4Vectors, tidyr, tools, yaml Suggests: testthat, knitr, rmarkdown License: GPL-3 Package: riboSeqR Version: 1.38.0 Depends: R (>= 3.0.2), methods, GenomicRanges, abind Imports: Rsamtools, IRanges, S4Vectors, baySeq, GenomeInfoDb, seqLogo Suggests: BiocStyle, RUnit, BiocGenerics License: GPL-3 Package: ribosomeProfilingQC Version: 1.16.0 Depends: R (>= 4.0), GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, BSgenome, EDASeq, GenomicAlignments, GenomicFeatures, GenomeInfoDb, IRanges, methods, motifStack, rtracklayer, Rsamtools, RUVSeq, Rsubread, S4Vectors, XVector, ggplot2, ggfittext, scales, ggrepel, utils, cluster, stats, graphics, grid, txdbmaker, ggExtra Suggests: RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, edgeR, DESeq2, limma, ashr, testthat, rmarkdown, vsn, Biobase License: GPL (>= 3) + file LICENSE Package: RImmPort Version: 1.32.0 Imports: plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools, utils, RSQLite Suggests: knitr License: GPL-3 Package: RIPAT Version: 1.14.0 Depends: R (>= 4.0) Imports: biomaRt (>= 2.38.0), GenomicRanges (>= 1.34.0), ggplot2 (>= 3.1.0), grDevices (>= 3.5.3), IRanges (>= 2.16.0), karyoploteR (>= 1.6.3), openxlsx (>= 4.1.4), plyr (>= 1.8.4), regioneR (>= 1.12.0), rtracklayer (>= 1.42.2), stats (>= 3.5.3), stringr (>= 1.3.1), utils (>= 3.5.3) Suggests: knitr (>= 1.28) License: Artistic-2.0 Package: RITAN Version: 1.28.0 Depends: R (>= 4.0), Imports: graphics, methods, stats, utils, grid, gridExtra, reshape2, gplots, ggplot2, plotrix, RColorBrewer, STRINGdb, MCL, linkcomm, dynamicTreeCut, gsubfn, hash, png, sqldf, igraph, BgeeDB, knitr, RITANdata, GenomicFeatures, ensembldb, AnnotationFilter, EnsDb.Hsapiens.v86 Suggests: rmarkdown, BgeeDB License: file LICENSE Package: RIVER Version: 1.28.0 Depends: R (>= 3.3.2) Imports: glmnet, pROC, ggplot2, graphics, stats, Biobase, methods, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools License: GPL (>= 2) Package: RJMCMCNucleosomes Version: 1.28.0 Depends: R (>= 3.5.0), IRanges, GenomicRanges Imports: Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, GenomeInfoDb, S4Vectors (>= 0.23.10), BiocParallel, stats, graphics, methods, grDevices LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, nucleoSim, RUnit License: Artistic-2.0 Archs: x64 Package: RLassoCox Version: 1.12.0 Depends: R (>= 4.1), glmnet Imports: Matrix, igraph, survival, stats Suggests: knitr License: Artistic-2.0 Package: RLMM Version: 1.66.0 Depends: R (>= 2.1.0) Imports: graphics, grDevices, MASS, stats, utils License: LGPL (>= 2) Package: RLSeq Version: 1.10.0 Depends: R (>= 4.2.0) Imports: dplyr, ggplot2, RColorBrewer, grid, regioneR, valr, caretEnsemble, GenomicFeatures, rtracklayer, GenomicRanges, GenomeInfoDb, ComplexHeatmap, AnnotationHub, VennDiagram, callr, circlize, ggplotify, ggprism, methods, stats, RLHub, aws.s3, pheatmap Suggests: AnnotationDbi, BiocStyle, covr, lintr, rcmdcheck, DT, httr, jsonlite, kableExtra, kernlab, knitr, magick, MASS, org.Hs.eg.db, R.utils, randomForest, readr, rmarkdown, rpart, testthat (>= 3.0.0), tibble, tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, futile.logger License: MIT + file LICENSE Package: Rmagpie Version: 1.60.0 Depends: R (>= 2.6.1), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab, methods, pamr, stats, utils Suggests: xtable License: GPL (>= 3) Package: RMassBank Version: 3.14.0 Depends: Rcpp Imports: XML,rjson,S4Vectors,digest, rcdk,yaml,mzR,methods,Biobase,MSnbase,httr, enviPat,assertthat,logger,readJDX,webchem, ChemmineR,ChemmineOB,R.utils,data.table,glue Suggests: BiocStyle,gplots,RMassBankData (>= 1.33.1), xcms (>= 1.37.1), CAMERA, RUnit, knitr, rmarkdown License: Artistic-2.0 Package: rmelting Version: 1.20.0 Depends: R (>= 3.6) Imports: Rdpack, rJava (>= 0.9-8) Suggests: readxl, knitr, rmarkdown, reshape2, pander, testthat License: GPL-2 | GPL-3 Package: Rmmquant Version: 1.22.0 Depends: R (>= 3.6) Imports: Rcpp (>= 0.12.8), methods, S4Vectors, GenomicRanges, SummarizedExperiment, devtools, TBX20BamSubset, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, DESeq2, apeglm, BiocStyle LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 Archs: x64 Package: rmspc Version: 1.10.0 Imports: processx, BiocManager, rtracklayer, stats, tools, methods, GenomicRanges, stringr Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 Package: RNAAgeCalc Version: 1.16.0 Depends: R (>= 3.6) Imports: ggplot2, recount, impute, AnnotationDbi, org.Hs.eg.db, stats, SummarizedExperiment, methods Suggests: knitr, rmarkdown, testthat License: GPL-2 Package: RNAdecay Version: 1.24.0 Depends: R (>= 3.5) Imports: stats, grDevices, grid, ggplot2, gplots, utils, TMB, nloptr, scales Suggests: parallel, knitr, reshape2, rmarkdown License: GPL-2 Archs: x64 Package: rnaEditr Version: 1.14.0 Depends: R (>= 4.0) Imports: GenomicRanges, IRanges, BiocGenerics, GenomeInfoDb, bumphunter, S4Vectors, stats, survival, logistf, plyr, corrplot Suggests: knitr, rmarkdown, testthat License: GPL-3 Package: RNAinteract Version: 1.52.0 Depends: R (>= 2.12.0), Imports: RColorBrewer, ICS, ICSNP, cellHTS2, geneplotter, gplots, grid, hwriter, lattice, latticeExtra, limma, methods, splots (>= 1.13.12), abind, locfit, Biobase License: Artistic-2.0 Package: RNAmodR Version: 1.18.0 Depends: R (>= 4.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomicRanges, Modstrings Imports: methods, stats, grDevices, matrixStats, BiocGenerics, Biostrings (>= 2.57.2), BiocParallel, txdbmaker, GenomicFeatures, GenomicAlignments, GenomeInfoDb, rtracklayer, Rsamtools, BSgenome, RColorBrewer, colorRamps, ggplot2, Gviz (>= 1.31.0), reshape2, graphics, ROCR Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data License: Artistic-2.0 Package: RNAmodR.AlkAnilineSeq Version: 1.18.0 Depends: R (>= 4.0), RNAmodR (>= 1.5.3) Imports: methods, S4Vectors, IRanges, BiocGenerics, GenomicRanges, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, Biostrings, RNAmodR.Data License: Artistic-2.0 Package: RNAmodR.ML Version: 1.18.0 Depends: R (>= 3.6), RNAmodR Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, stats, ranger Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data, RNAmodR.AlkAnilineSeq, GenomicFeatures, Rsamtools, rtracklayer, keras License: Artistic-2.0 Package: RNAmodR.RiboMethSeq Version: 1.18.0 Depends: R (>= 4.0), RNAmodR (>= 1.5.3) Imports: methods, S4Vectors, BiocGenerics, IRanges, GenomicRanges, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, RNAmodR.Data License: Artistic-2.0 Package: RNAsense Version: 1.18.0 Depends: R (>= 3.6) Imports: ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment, stats, utils, methods Suggests: knitr, rmarkdown License: GPL-3 Package: rnaseqcomp Version: 1.34.0 Depends: R (>= 3.2.0) Imports: RColorBrewer, methods Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 Package: RNAseqCovarImpute Version: 1.2.0 Depends: R (>= 4.3.0) Imports: Biobase, BiocGenerics, BiocParallel, stats, limma, dplyr, magrittr, rlang, edgeR, foreach, mice Suggests: BiocStyle, knitr, PCAtools, rmarkdown, tidyr, stringr, testthat (>= 3.0.0) License: GPL-3 Package: RNASeqPower Version: 1.44.0 License: LGPL (>= 2) Package: RnaSeqSampleSize Version: 2.14.0 Depends: R (>= 4.0.0), ggplot2, RnaSeqSampleSizeData Imports: biomaRt,edgeR,heatmap3,matlab,KEGGREST,methods,grDevices, graphics, stats, Rcpp (>= 0.11.2),recount,ggpubr,SummarizedExperiment,tidyr,dplyr,tidyselect,utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) Archs: x64 Package: RnBeads Version: 2.22.0 Depends: R (>= 3.0.0), BiocGenerics, S4Vectors (>= 0.9.25), GenomicRanges, MASS, cluster, ff, fields, ggplot2 (>= 0.9.2), gplots, grid, gridExtra, limma, matrixStats, methods, illuminaio, methylumi, plyr Imports: IRanges Suggests: Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RnBeads.hg19, RnBeads.mm9, RnBeads.hg38, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit, MethylSeekR, sesame License: GPL-3 Package: Rnits Version: 1.38.0 Depends: R (>= 3.6.0), Biobase, ggplot2, limma, methods Imports: affy, boot, impute, splines, graphics, qvalue, reshape2 Suggests: BiocStyle, knitr, GEOquery, stringr License: GPL-3 Package: roar Version: 1.40.0 Depends: R (>= 3.0.1) Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, GenomicAlignments (>= 0.99.4), rtracklayer, GenomeInfoDb Suggests: RNAseqData.HNRNPC.bam.chr14, testthat License: GPL-3 Package: roastgsa Version: 1.2.0 Depends: R (>= 4.3.0) Imports: parallel, grDevices, graphics, utils, stats, methods, grid, RColorBrewer, gplots, ggplot2, limma, Biobase Suggests: BiocStyle, knitr, rmarkdown, GSEABenchmarkeR, EnrichmentBrowser, preprocessCore, DESeq2 License: GPL-3 Package: ROC Version: 1.80.0 Depends: R (>= 1.9.0), utils, methods Imports: knitr Suggests: rmarkdown, Biobase, BiocStyle License: Artistic-2.0 Archs: x64 Package: ROCpAI Version: 1.16.0 Depends: boot, SummarizedExperiment, fission, knitr, methods Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 Package: RolDE Version: 1.8.0 Depends: R (>= 4.2.0) Imports: stats, methods, ROTS, matrixStats, foreach, parallel, doParallel, doRNG, rngtools, SummarizedExperiment, nlme, qvalue, grDevices, graphics, utils Suggests: knitr, printr, rmarkdown, testthat License: GPL-3 Package: rols Version: 3.0.0 Depends: methods Imports: httr2, jsonlite, utils, Biobase, BiocGenerics (>= 0.23.1) Suggests: GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), testthat, lubridate, DT, rmarkdown, License: GPL-2 Package: ROntoTools Version: 2.32.0 Depends: methods, graph, boot, KEGGREST, KEGGgraph, Rgraphviz Suggests: RUnit, BiocGenerics License: CC BY-NC-ND 4.0 + file LICENSE Package: ropls Version: 1.36.0 Depends: R (>= 3.5.0) Imports: Biobase, ggplot2, graphics, grDevices, methods, plotly, stats, MultiAssayExperiment, MultiDataSet, SummarizedExperiment, utils Suggests: BiocGenerics, BiocStyle, knitr, multtest, omicade4, rmarkdown, testthat License: CeCILL Package: ROSeq Version: 1.16.0 Depends: R (>= 4.0) Imports: pbmcapply, edgeR, limma Suggests: knitr, rmarkdown, testthat, RUnit, BiocGenerics License: GPL-3 Package: ROTS Version: 1.32.0 Depends: R (>= 3.3) Imports: Rcpp, stats, Biobase, methods LinkingTo: Rcpp Suggests: testthat License: GPL (>= 2) Archs: x64 Package: RPA Version: 1.60.0 Depends: R (>= 3.1.1), affy, BiocGenerics, BiocStyle, methods, rmarkdown Imports: phyloseq Suggests: knitr, parallel License: BSD_2_clause + file LICENSE Package: rprimer Version: 1.8.0 Depends: R (>= 4.1) Imports: Biostrings, bslib, DT, ggplot2, IRanges, mathjaxr, methods, patchwork, reshape2, S4Vectors, shiny, shinycssloaders, shinyFeedback Suggests: BiocStyle, covr, kableExtra, knitr, rmarkdown, styler, testthat (>= 3.0.0) License: GPL-3 Package: RProtoBufLib Version: 2.16.0 Suggests: knitr, rmarkdown License: BSD_3_clause Archs: x64 Package: rpx Version: 2.12.0 Depends: R (>= 3.5.0), methods Imports: BiocFileCache, jsonlite, xml2, RCurl, curl, utils Suggests: Biostrings, BiocStyle, testthat, knitr, tibble, rmarkdown License: GPL-2 Package: Rqc Version: 1.38.0 Depends: BiocParallel, ShortRead, ggplot2 Imports: BiocGenerics (>= 0.25.1), Biostrings, IRanges, methods, S4Vectors, knitr (>= 1.7), BiocStyle, plyr, markdown, grid, reshape2, Rcpp (>= 0.11.6), biovizBase, shiny, Rsamtools, GenomicAlignments, GenomicFiles LinkingTo: Rcpp Suggests: rmarkdown, testthat License: GPL (>= 2) Archs: x64 Package: rqubic Version: 1.50.0 Imports: methods, Biobase, BiocGenerics, biclust Suggests: RColorBrewer License: GPL-2 Archs: x64 Package: rRDP Version: 1.38.0 Depends: Biostrings (>= 2.26.2) Imports: rJava, utils Suggests: rRDPData, knitr, rmarkdown License: GPL-2 + file LICENSE Package: RRHO Version: 1.44.0 Depends: R (>= 2.10), grid Imports: VennDiagram Suggests: lattice License: GPL-2 Package: rrvgo Version: 1.16.0 Imports: GOSemSim, AnnotationDbi, GO.db, pheatmap, ggplot2, ggrepel, treemap, tm, wordcloud, shiny, grDevices, grid, stats, methods, umap Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), shinydashboard, DT, plotly, heatmaply, magrittr, utils, clusterProfiler, DOSE, slam, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db License: GPL-3 Package: Rsamtools Version: 2.20.0 Depends: methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Biostrings (>= 2.47.6), R (>= 3.5.0) Imports: utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector (>= 0.19.7), zlibbioc, bitops, BiocParallel, stats LinkingTo: Rhtslib (>= 2.99.1), S4Vectors, IRanges, XVector, Biostrings Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr License: Artistic-2.0 | file LICENSE Archs: x64 Package: rsbml Version: 2.62.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils Imports: BiocGenerics, graph, utils License: Artistic-2.0 Archs: x64 Package: rScudo Version: 1.20.0 Depends: R (>= 3.6) Imports: methods, stats, igraph, stringr, grDevices, Biobase, S4Vectors, SummarizedExperiment, BiocGenerics Suggests: testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret, e1071, parallel, doParallel License: GPL-3 Package: rsemmed Version: 1.14.0 Depends: R (>= 4.0), igraph Imports: methods, magrittr, stringr, dplyr Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 Package: RSeqAn Version: 1.24.0 License: BSD_3_clause + file LICENSE Package: Rsubread Version: 2.18.0 Imports: grDevices, stats, utils, Matrix License: GPL (>= 3) Archs: x64 Package: RSVSim Version: 1.44.0 Depends: R (>= 3.5.0), Biostrings, GenomicRanges Imports: methods, IRanges, ShortRead Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer, pwalign License: LGPL-3 Package: rSWeeP Version: 1.16.0 Depends: R (>= 4.0) Imports: pracma, stats Suggests: Biostrings, methods, knitr, rmarkdown, BiocStyle License: GPL-3 Package: RTCA Version: 1.56.0 Depends: methods,stats,graphics,Biobase,RColorBrewer, gtools Suggests: xtable License: LGPL-3 Package: RTCGA Version: 1.34.0 Depends: R (>= 3.3.0) Imports: XML, RCurl, assertthat, stringi, rvest, data.table, xml2, dplyr, purrr, survival, survminer, ggplot2, ggthemes, viridis, knitr, scales, rmarkdown, htmltools Suggests: devtools, testthat, pander, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, magrittr, tidyr License: GPL-2 Package: RTCGAToolbox Version: 2.34.0 Depends: R (>= 4.3.0) Imports: BiocGenerics, data.table, DelayedArray, GenomicRanges, GenomeInfoDb, httr, methods, RaggedExperiment, RCurl, RJSONIO, rvest, S4Vectors (>= 0.23.10), stats, stringr, SummarizedExperiment, TCGAutils (>= 1.9.4), utils Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown License: GPL-2 Package: RTN Version: 2.28.0 Depends: R (>= 3.6.3), methods, Imports: RedeR, minet, viper, mixtools, snow, stats, limma, data.table, IRanges, igraph, S4Vectors, SummarizedExperiment, car, pwr, pheatmap, grDevices, graphics, utils Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 Package: RTNduals Version: 1.28.0 Depends: R(>= 3.6.3), RTN(>= 2.14.1), methods Imports: graphics, grDevices, stats, utils Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 Package: RTNsurvival Version: 1.28.0 Depends: R(>= 3.6.3), RTN(>= 2.14.1), RTNduals(>= 1.14.1), methods Imports: survival, RColorBrewer, grDevices, graphics, stats, utils, scales, data.table, egg, ggplot2, pheatmap, dunn.test Suggests: Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 Package: RTopper Version: 1.50.0 Depends: R (>= 2.12.0), Biobase Imports: limma, multtest Suggests: org.Hs.eg.db, KEGGREST, GO.db License: GPL (>= 3) + file LICENSE Package: Rtpca Version: 1.14.0 Depends: R (>= 4.0.0), stats, dplyr, tidyr Imports: Biobase, methods, ggplot2, pROC, fdrtool, splines, utils, tibble Suggests: knitr, BiocStyle, TPP, testthat, rmarkdown License: GPL-3 Package: rtracklayer Version: 1.64.0 Depends: R (>= 3.5.0), methods, GenomicRanges (>= 1.37.2) Imports: XML (>= 1.98-0), BiocGenerics (>= 0.35.3), S4Vectors (>= 0.23.18), IRanges (>= 2.13.13), XVector (>= 0.19.7), GenomeInfoDb (>= 1.15.2), Biostrings (>= 2.47.6), zlibbioc, curl, httr, Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6), BiocIO, tools, restfulr (>= 0.0.13) LinkingTo: S4Vectors, IRanges, XVector Suggests: BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit License: Artistic-2.0 + file LICENSE Archs: x64 Package: Rtreemix Version: 1.66.0 Depends: R (>= 2.5.0) Imports: methods, graph, Biobase, Hmisc Suggests: Rgraphviz License: LGPL Archs: x64 Package: rTRM Version: 1.42.0 Depends: R (>= 2.10), igraph (>= 1.0) Imports: methods, AnnotationDbi, DBI, RSQLite Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2, BiocStyle, knitr, rmarkdown License: GPL-3 Package: rTRMui Version: 1.42.0 Imports: shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 Package: runibic Version: 1.26.0 Depends: R (>= 3.4.0), biclust, SummarizedExperiment Imports: Rcpp (>= 0.12.12), testthat, methods LinkingTo: Rcpp Suggests: knitr, rmarkdown, GEOquery, affy, airway, QUBIC License: MIT + file LICENSE Archs: x64 Package: RUVcorr Version: 1.36.0 Imports: corrplot, MASS, stats, lattice, grDevices, gridExtra, snowfall, psych, BiocParallel, grid, bladderbatch, reshape2, graphics Suggests: knitr, hgu133a2.db, rmarkdown License: GPL-2 Package: RUVnormalize Version: 1.38.0 Depends: R (>= 2.10.0) Imports: RUVnormalizeData, Biobase Enhances: spams License: GPL-3 Package: RUVSeq Version: 1.38.0 Depends: Biobase, EDASeq (>= 1.99.1), edgeR Imports: methods, MASS Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2 License: Artistic-2.0 Package: Rvisdiff Version: 1.2.0 Depends: R (>= 4.3.0) Imports: edgeR, utils Suggests: knitr, rmarkdown, DESeq2, limma, SummarizedExperiment, airway, BiocStyle, matrixTests, BiocManager License: GPL-2 | GPL-3 Package: RVS Version: 1.26.0 Depends: R (>= 3.5.0) Imports: GENLIB, gRain, snpStats, kinship2, methods, stats, utils, R.utils Suggests: knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation License: GPL-2 Package: rWikiPathways Version: 1.24.0 Imports: httr, utils, XML, rjson, data.table, RCurl, dplyr, tidyr, readr, stringr, purrr, lubridate Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE Package: S4Arrays Version: 1.4.1 Depends: R (>= 4.3.0), methods, Matrix, abind, BiocGenerics (>= 0.45.2), S4Vectors, IRanges Imports: stats, crayon LinkingTo: S4Vectors Suggests: BiocParallel, SparseArray (>= 0.0.4), DelayedArray, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 Archs: x64 Package: S4Vectors Version: 0.42.1 Depends: R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>= 0.37.0) Suggests: IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle, knitr License: Artistic-2.0 Archs: x64 Package: safe Version: 3.44.0 Depends: R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM Suggests: GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats License: GPL (>= 2) Package: sagenhaft Version: 1.74.0 Depends: R (>= 2.10), SparseM (>= 0.73), methods Imports: graphics, stats, utils License: GPL (>= 2) Package: SAIGEgds Version: 2.4.0 Depends: R (>= 3.5.0), gdsfmt (>= 1.28.0), SeqArray (>= 1.42.3), Rcpp Imports: methods, stats, utils, Matrix, RcppParallel, CompQuadForm, survey LinkingTo: Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0) Suggests: parallel, markdown, rmarkdown, crayon, SNPRelate, RUnit, knitr, ggmanh, BiocGenerics License: GPL-3 Archs: x64 Package: sampleClassifier Version: 1.28.0 Depends: R (>= 4.0), MGFM, MGFR, annotate Imports: e1071, ggplot2, stats, utils Suggests: sampleClassifierData, BiocStyle, hgu133a.db, hgu133plus2.db License: Artistic-2.0 Package: SamSPECTRAL Version: 1.58.0 Depends: R (>= 3.3.3) Imports: methods License: GPL (>= 2) Archs: x64 Package: sangeranalyseR Version: 1.14.0 Depends: R (>= 4.0.0), stringr, ape, Biostrings, pwalign, DECIPHER, parallel, reshape2, sangerseqR, gridExtra, shiny, shinydashboard, shinyjs, data.table, plotly, DT, zeallot, excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx, tools, rmarkdown (>= 2.9), knitr (>= 1.33), seqinr, BiocStyle, logger Suggests: testthat (>= 2.1.0) License: GPL-2 Package: sangerseqR Version: 1.40.0 Depends: R (>= 3.5.0), Biostrings, pwalign, stringr Imports: methods, shiny Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-2 Package: SARC Version: 1.2.0 Depends: R (>= 4.3), RaggedExperiment, GenomicRanges Imports: tidyverse, utils, reshape2, DescTools, metap, multtest, plyranges, data.table, scales, RColorBrewer, grid, gtable, gridExtra, GenomicFeatures, stats, ggplot2, plotly, IRanges Suggests: knitr, kableExtra, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, Homo.sapiens, TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus, GenomicAlignments License: GPL-3 Package: sarks Version: 1.16.0 Depends: R (>= 4.0) Imports: rJava, Biostrings, IRanges, utils, stats, cluster, binom Suggests: RUnit, BiocGenerics, ggplot2 License: BSD_3_clause + file LICENSE Package: saseR Version: 1.0.0 Depends: R (>= 4.3.0) Imports: ASpli, S4Vectors, BiocGenerics, GenomicFeatures, MASS, PRROC, SummarizedExperiment, edgeR, pracma, precrec, BiocParallel, DESeq2, DEXSeq, data.table, limma, methods, GenomicRanges, GenomicAlignments, rrcov, MatrixGenerics, stats, IRanges, knitr, dplyr, igraph, parallel License: Artistic-2.0 Package: satuRn Version: 1.12.0 Depends: R (>= 4.1) Imports: locfdr, SummarizedExperiment, BiocParallel, limma, pbapply, ggplot2, boot, Matrix, stats, methods, graphics Suggests: knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub, ensembldb, edgeR, DEXSeq, stageR, DelayedArray License: Artistic-2.0 Package: SBGNview Version: 1.18.0 Depends: R (>= 3.6), pathview, SBGNview.data Imports: Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph, rmarkdown, knitr, SummarizedExperiment, AnnotationDbi, httr, KEGGREST, bookdown Suggests: testthat, gage License: AGPL-3 Package: SBMLR Version: 2.0.0 Depends: XML, deSolve Suggests: rsbml License: GPL-2 Package: SC3 Version: 1.32.0 Depends: R(>= 3.3) Imports: graphics, stats, utils, methods, e1071, parallel, foreach, doParallel, doRNG, shiny, ggplot2, pheatmap (>= 1.0.8), ROCR, robustbase, rrcov, cluster, WriteXLS, Rcpp (>= 0.11.1), SummarizedExperiment, SingleCellExperiment, BiocGenerics, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, mclust, scater, BiocStyle License: GPL-3 Archs: x64 Package: Scale4C Version: 1.26.0 Depends: R (>= 3.4), smoothie, GenomicRanges, IRanges, SummarizedExperiment Imports: methods, grDevices, graphics, utils License: LGPL-3 Package: ScaledMatrix Version: 1.12.0 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular, DelayedMatrixStats License: GPL-3 Package: scanMiR Version: 1.10.0 Depends: R (>= 4.0) Imports: Biostrings, pwalign, GenomicRanges, IRanges, data.table, BiocParallel, methods, GenomeInfoDb, S4Vectors, ggplot2, stats, stringi, utils, graphics, grid, seqLogo, cowplot Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 Package: scanMiRApp Version: 1.10.0 Depends: R (>= 4.0), scanMiR Imports: AnnotationDbi, AnnotationFilter, AnnotationHub, BiocParallel, Biostrings, data.table, digest, DT, ensembldb, fst, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, IRanges, Matrix, methods, plotly, rintrojs, rtracklayer, S4Vectors, scanMiRData, shiny, shinycssloaders, shinydashboard, shinyjqui, stats, utils, txdbmaker, waiter Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-3 Package: scAnnotatR Version: 1.10.0 Depends: R (>= 4.1), Seurat, SingleCellExperiment, SummarizedExperiment Imports: dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats, e1071, ape, kernlab, AnnotationHub, utils Suggests: knitr, rmarkdown, scRNAseq, testthat License: MIT + file LICENSE Package: SCAN.UPC Version: 2.46.0 Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach, sva Imports: utils, methods, MASS, tools, IRanges Suggests: pd.hg.u95a License: MIT Package: SCANVIS Version: 1.18.0 Depends: R (>= 3.6) Imports: IRanges,plotrix,RCurl,rtracklayer Suggests: knitr, rmarkdown License: file LICENSE Package: SCArray Version: 1.12.0 Depends: R (>= 3.5.0), gdsfmt (>= 1.36.0), methods, DelayedArray (>= 0.28.0) Imports: S4Vectors, utils, Matrix, BiocParallel, DelayedMatrixStats, SummarizedExperiment, SingleCellExperiment, BiocSingular Suggests: BiocGenerics, scater, scuttle, uwot, RUnit, knitr, markdown, rmarkdown, rhdf5, HDF5Array License: GPL-3 Archs: x64 Package: SCArray.sat Version: 1.4.0 Depends: methods, SCArray (>= 1.7.13), SeuratObject (>= 5.0), Seurat (>= 5.0) Imports: S4Vectors, utils, stats, BiocGenerics, BiocParallel, gdsfmt, DelayedArray, BiocSingular, SummarizedExperiment, Matrix Suggests: future, RUnit, knitr, markdown, rmarkdown, BiocStyle License: GPL-3 Package: scater Version: 1.32.0 Depends: SingleCellExperiment, scuttle, ggplot2 Imports: stats, utils, methods, Matrix, BiocGenerics, S4Vectors, SummarizedExperiment, DelayedArray, MatrixGenerics, beachmat, BiocNeighbors, BiocSingular, BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, RColorBrewer, RcppML, uwot, pheatmap, ggrepel, ggrastr Suggests: BiocStyle, snifter, densvis, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore License: GPL-3 Package: scatterHatch Version: 1.10.0 Depends: R (>= 4.1) Imports: grid, ggplot2, plyr, spatstat.geom, stats, grDevices Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE Package: scBFA Version: 1.18.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, Seurat, MASS, zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods, Matrix Suggests: knitr, rmarkdown, testthat, Rtsne License: GPL-3 + file LICENSE Package: SCBN Version: 1.22.0 Depends: R (>= 3.5.0) Imports: stats Suggests: knitr,rmarkdown,BiocStyle,BiocManager License: GPL-2 Package: scBubbletree Version: 1.6.0 Depends: R (>= 4.2.0) Imports: reshape2, future, future.apply, ape, scales, Seurat, ggplot2, ggtree, patchwork, proxy, methods, stats, base, utils Suggests: BiocStyle, knitr, testthat, cluster, SingleCellExperiment License: GPL-3 + file LICENSE Package: scCB2 Version: 1.14.0 Depends: R (>= 3.6.0) Imports: SingleCellExperiment, SummarizedExperiment, Matrix, methods, utils, stats, edgeR, rhdf5, parallel, DropletUtils, doParallel, iterators, foreach, Seurat Suggests: testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle, rmarkdown License: GPL-3 Package: scClassify Version: 1.16.0 Depends: R (>= 4.0) Imports: S4Vectors, limma, ggraph, igraph, methods, cluster, minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix, ggplot2, hopach, diptest, mgcv, stats, graphics, statmod, Cepo Suggests: knitr, rmarkdown, BiocStyle, pkgdown License: GPL-3 Package: sccomp Version: 1.8.0 Depends: R (>= 4.2.0) Imports: methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstantools (>= 2.1.1), rstan (>= 2.26.0), SeuratObject, SingleCellExperiment, parallel, dplyr, tidyr, purrr, magrittr, rlang, tibble, boot, lifecycle, stats, tidyselect, utils, ggplot2, ggrepel, patchwork, forcats, readr, scales, stringr, glue LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.26.0), StanHeaders (>= 2.26.0) Suggests: BiocStyle, testthat (>= 3.0.0), markdown, knitr, loo, tidyseurat, tidySingleCellExperiment, prettydoc Enhances: furrr, extraDistr License: GPL-3 Archs: x64 Package: scDataviz Version: 1.14.0 Depends: R (>= 4.0), S4Vectors, SingleCellExperiment, Imports: ggplot2, ggrepel, flowCore, umap, Seurat, reshape2, scales, RColorBrewer, corrplot, stats, grDevices, graphics, utils, MASS, matrixStats, methods Suggests: PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra, rmarkdown License: GPL-3 Package: scDblFinder Version: 1.18.0 Depends: R (>= 4.0), SingleCellExperiment Imports: igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, scran, scater, scuttle, bluster, methods, DelayedArray, xgboost, stats, utils, MASS, IRanges, GenomicRanges, GenomeInfoDb, Rsamtools, rtracklayer Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans License: GPL-3 + file LICENSE Package: scDD Version: 1.28.0 Depends: R (>= 3.5.0) Imports: fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm, SingleCellExperiment, SummarizedExperiment, grDevices, graphics, stats, S4Vectors, scran Suggests: BiocStyle, knitr, gridExtra License: GPL-2 Package: scDDboost Version: 1.6.0 Depends: R (>= 4.2), ggplot2 Imports: Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0),EBSeq, BiocParallel, mclust, SingleCellExperiment, cluster, Oscope, SummarizedExperiment, stats, methods LinkingTo: Rcpp, RcppEigen, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) Archs: x64 Package: scde Version: 2.32.0 Depends: R (>= 3.0.0), flexmix Imports: Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook, rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods, nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown License: GPL-2 Archs: x64 Package: scDesign3 Version: 1.2.0 Depends: R (>= 4.3.0) Imports: dplyr, tibble, stats, methods, mgcv, gamlss, gamlss.dist, SummarizedExperiment, SingleCellExperiment, mclust, mvtnorm, parallel, pbmcapply, rvinecopulib, umap, ggplot2, irlba, viridis, BiocParallel, matrixStats, Matrix, sparseMVN, coop Suggests: mvnfast, igraph, knitr, rmarkdown, testthat (>= 3.0.0), RefManageR, sessioninfo, BiocStyle License: MIT + file LICENSE Package: scds Version: 1.20.0 Depends: R (>= 3.6.0) Imports: Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment, xgboost, methods, stats, dplyr, pROC Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown License: MIT + file LICENSE Package: SCFA Version: 1.14.0 Depends: R (>= 4.0) Imports: matrixStats, BiocParallel, torch (>= 0.3.0), coro, igraph, Matrix, cluster, psych, glmnet, RhpcBLASctl, stats, utils, methods, survival Suggests: knitr, rmarkdown, BiocStyle License: LGPL Package: scFeatureFilter Version: 1.24.0 Depends: R (>= 3.6) Imports: dplyr (>= 0.7.3), ggplot2 (>= 2.1.0), magrittr (>= 1.5), rlang (>= 0.1.2), tibble (>= 1.3.4), stats, methods Suggests: testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot License: MIT + file LICENSE Package: scFeatures Version: 1.4.0 Depends: R (>= 4.2.0) Imports: DelayedArray, DelayedMatrixStats, EnsDb.Hsapiens.v79, EnsDb.Mmusculus.v79, GSVA, ape, glue, dplyr, ensembldb, gtools, msigdbr, proxyC, reshape2, spatstat.explore, spatstat.geom, tidyr, AUCell, BiocParallel, rmarkdown, methods, stats, cli, SingleCellSignalR, MatrixGenerics, Seurat, DT Suggests: knitr, S4Vectors, survival, survminer, BiocStyle, ClassifyR, org.Hs.eg.db, clusterProfiler License: GPL-3 Package: scGPS Version: 1.18.0 Depends: R (>= 3.6), SummarizedExperiment, dynamicTreeCut, SingleCellExperiment Imports: glmnet (> 2.0), caret (>= 6.0), ggplot2 (>= 2.2.1), fastcluster, dplyr, Rcpp, RcppArmadillo, RcppParallel, grDevices, graphics, stats, utils, DESeq2, locfit LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown, RColorBrewer, ReactomePA, clusterProfiler, cowplot, org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne, BiocParallel, e1071, WGCNA, devtools, DOSE License: GPL-3 Archs: x64 Package: schex Version: 1.18.0 Depends: SingleCellExperiment (>= 1.7.4), ggplot2 (>= 3.2.1) Imports: hexbin, stats, methods, cluster, dplyr, entropy, ggforce, grid, rlang, concaveman Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, Seurat, shinydashboard, iSEE, igraph, scran, tibble, scuttle License: GPL-3 Package: scHOT Version: 1.16.0 Depends: R (>= 4.0) Imports: S4Vectors (>= 0.24.3), SingleCellExperiment, Matrix, SummarizedExperiment, IRanges, methods, stats, BiocParallel, reshape, ggplot2, igraph, grDevices, ggforce, graphics Suggests: knitr, markdown, rmarkdown, scater, scattermore, scales, matrixStats, deldir License: GPL-3 Package: scider Version: 1.2.0 Depends: R (>= 4.3) Imports: SpatialExperiment, SummarizedExperiment, spatstat.geom, spatstat.explore, sf, lwgeom, ggplot2, stats, pheatmap, plotly, shiny, igraph, janitor, knitr, methods, utils, rlang, isoband, S4Vectors, grDevices Suggests: edgeR, testthat (>= 3.0.0) License: GPL-3 + file LICENSE Package: scifer Version: 1.6.0 Imports: dplyr, rmarkdown, data.table, Biostrings, parallel, stats, plyr, knitr, ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra, tibble, scales, rlang, flowCore, methods Suggests: fs, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE Package: scmap Version: 1.26.0 Depends: R(>= 3.4) Imports: Biobase, SingleCellExperiment, SummarizedExperiment, BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy, utils, googleVis, ggplot2, methods, stats, e1071, randomForest, Rcpp (>= 0.12.12) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 Archs: x64 Package: scMerge Version: 1.20.0 Depends: R (>= 3.6.0) Imports: BiocParallel, BiocSingular, BiocNeighbors, cluster, DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop (>= 1.9.4), proxyC, ruv, cvTools, scater, batchelor, scran, methods, S4Vectors (>= 0.23.19), SingleCellExperiment (>= 1.7.3), SummarizedExperiment Suggests: BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, proxy, testthat, badger License: GPL-3 Package: scMET Version: 1.6.0 Depends: R (>= 4.2.0) Imports: methods, Rcpp (>= 1.0.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), rstantools (>= 2.1.0), VGAM, data.table, MASS, logitnorm, ggplot2, matrixStats, assertthat, viridis, coda, BiocStyle, cowplot, stats, SummarizedExperiment, SingleCellExperiment, Matrix, dplyr, S4Vectors LinkingTo: BH (>= 1.66.0), Rcpp (>= 1.0.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), StanHeaders (>= 2.21.0.7) Suggests: testthat, knitr, rmarkdown License: GPL-3 Archs: x64 Package: scmeth Version: 1.24.0 Depends: R (>= 3.5.0) Imports: knitr, rmarkdown, bsseq, AnnotationHub, GenomicRanges, reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15), annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb, Biostrings, DT, HDF5Array (>= 1.7.5) Suggests: BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes License: GPL-2 Package: scMitoMut Version: 1.0.0 Depends: R (>= 4.3.0) Imports: data.table, Rcpp, magrittr, plyr, stringr, utils, stats, methods, ggplot2, pheatmap, zlibbioc, RColorBrewer, rhdf5, readr, parallel, grDevices LinkingTo: Rcpp, RcppArmadillo Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM, R.utils License: Artistic-2.0 Archs: x64 Package: scMultiSim Version: 1.0.0 Depends: R (>= 4.4.0) Imports: foreach, rlang, dplyr, ggplot2, Rtsne, ape, MASS, matrixStats, phytools, KernelKnn, gplots, zeallot, crayon, assertthat, igraph, methods, grDevices, graphics, stats, utils, markdown, SummarizedExperiment Suggests: knitr, rmarkdown, roxygen2, testthat (>= 3.0.0) License: Artistic-2.0 Package: SCnorm Version: 1.26.0 Depends: R (>= 3.4.0), Imports: SingleCellExperiment, SummarizedExperiment, stats, methods, graphics, grDevices, parallel, quantreg, cluster, moments, data.table, BiocParallel, S4Vectors, ggplot2, forcats, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL (>= 2) Package: scone Version: 1.28.0 Depends: R (>= 3.4), methods, SummarizedExperiment Imports: graphics, stats, utils, aroma.light, BiocParallel, class, cluster, compositions, diptest, edgeR, fpc, gplots, grDevices, hexbin, limma, matrixStats, mixtools, RColorBrewer, boot, rhdf5, RUVSeq, rARPACK, MatrixGenerics, SingleCellExperiment Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData License: Artistic-2.0 Package: Sconify Version: 1.24.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 Package: SCOPE Version: 1.16.0 Depends: R (>= 3.6.0), GenomicRanges, IRanges, Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19 Imports: stats, grDevices, graphics, utils, DescTools, RColorBrewer, gplots, foreach, parallel, doParallel, DNAcopy, BSgenome, Biostrings, BiocGenerics, S4Vectors Suggests: knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0) License: GPL-2 Package: scoreInvHap Version: 1.26.0 Depends: R (>= 3.6.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE Package: scp Version: 1.14.0 Depends: R (>= 4.3.0), QFeatures (>= 1.13.5) Imports: dplyr, IHW, ggplot2, ggrepel, matrixStats, metapod, methods, MsCoreUtils, MultiAssayExperiment, nipals, RColorBrewer, S4Vectors, SingleCellExperiment, SummarizedExperiment, stats, utils Suggests: BiocStyle, MsDataHub (>= 1.3.3), impute, knitr, patchwork, preprocessCore, rmarkdown, scater, scpdata, sva, testthat, vsn, uwot License: Artistic-2.0 Package: scPCA Version: 1.18.0 Depends: R (>= 4.0.0) Imports: stats, methods, assertthat, tibble, dplyr, purrr, stringr, Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca, cluster, kernlab, origami, RSpectra, coop, Matrix, DelayedArray, ScaledMatrix, MatrixGenerics Suggests: DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter, SingleCellExperiment, microbenchmark License: MIT + file LICENSE Package: scPipe Version: 2.4.0 Depends: R (>= 4.2.0), SingleCellExperiment Imports: AnnotationDbi, basilisk, BiocGenerics, biomaRt, Biostrings, data.table, dplyr, DropletUtils, flexmix, GenomicRanges, GenomicAlignments, GGally, ggplot2, glue (>= 1.3.0), grDevices, graphics, hash, IRanges, magrittr, MASS, Matrix (>= 1.5.0), mclust, methods, MultiAssayExperiment, org.Hs.eg.db, org.Mm.eg.db, purrr, Rcpp (>= 0.11.3), reshape, reticulate, Rhtslib, rlang, robustbase, Rsamtools, Rsubread, rtracklayer, SummarizedExperiment, S4Vectors, scales, stats, stringr, tibble, tidyr, tools, utils, vctrs (>= 0.5.2) LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc, testthat Suggests: BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra, knitr, locStra, plotly, rmarkdown, RColorBrewer, readr, reshape2, RANN, shiny, scater (>= 1.11.0), testthat, xml2, umap License: GPL (>= 2) Archs: x64 Package: scran Version: 1.32.0 Depends: SingleCellExperiment, scuttle Imports: SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, edgeR, limma, igraph, statmod, DelayedArray, DelayedMatrixStats, BiocSingular, bluster, metapod, dqrng, beachmat LinkingTo: Rcpp, beachmat, BH, dqrng, scuttle Suggests: testthat, BiocStyle, knitr, rmarkdown, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, pheatmap, scater License: GPL-3 Archs: x64 Package: scReClassify Version: 1.10.0 Depends: R (>= 4.1) Imports: randomForest, e1071, stats, SummarizedExperiment, SingleCellExperiment, methods Suggests: testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr License: GPL-3 + file LICENSE Package: scRecover Version: 1.20.0 Depends: R (>= 3.4.0) Imports: stats, utils, methods, graphics, doParallel, foreach, parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS (>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>= 4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), BiocParallel (>= 1.12.0) Suggests: knitr, rmarkdown, SingleCellExperiment, testthat License: GPL Package: screenCounter Version: 1.4.0 Depends: S4Vectors, SummarizedExperiment Imports: Rcpp, zlibbioc, BiocParallel LinkingTo: Rcpp Suggests: BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE Archs: x64 Package: ScreenR Version: 1.6.0 Depends: R (>= 4.2) Imports: methods (>= 4.0), rlang (>= 0.4), stringr (>= 1.4), limma (>= 3.46), patchwork (>= 1.1), tibble (>= 3.1.6), scales (>= 1.1.1), ggvenn (>= 0.1.9), purrr (>= 0.3.4), ggplot2 (>= 3.3), stats, tidyr (>= 1.2), magrittr (>= 1.0), dplyr (>= 1.0), edgeR (>= 3.32), tidyselect (>= 1.1.2) Suggests: rmarkdown (>= 2.11), knitr (>= 1.37), testthat (>= 3.0.0), BiocStyle (>= 2.22.0), covr (>= 3.5) License: MIT + file LICENSE Package: scRepertoire Version: 2.0.0 Depends: ggplot2, R (>= 4.0) Imports: cubature, dplyr, evmix, ggalluvial, ggdendro, ggraph, grDevices, igraph, iNEXT, methods, plyr, quantreg, Rcpp, reshape2, rjson, rlang, S4Vectors, SeuratObject, SingleCellExperiment, stats, stringr, stringdist, SummarizedExperiment, tidygraph, truncdist, utils, VGAM, hash LinkingTo: Rcpp Suggests: BiocManager, BiocStyle, circlize, knitr, rmarkdown, scales, scater, Seurat, spelling, testthat (>= 3.0.0), vdiffr License: MIT + file LICENSE Archs: x64 Package: scRNAseqApp Version: 1.4.0 Depends: R (>= 4.3.0) Imports: bibtex, bslib, circlize, ComplexHeatmap, data.table, DBI, DT, GenomicRanges, GenomeInfoDb, ggdendro, ggforce, ggplot2, ggrepel, ggridges, grDevices, grid, gridExtra, htmltools, IRanges, jsonlite, magrittr, methods, patchwork, plotly, RColorBrewer, RefManageR, rhdf5, Rsamtools, RSQLite, rtracklayer, S4Vectors, scales, scrypt, Seurat, SeuratObject, shiny, shinyhelper, shinymanager, slingshot, SingleCellExperiment, sortable, stats, tools, xfun, xml2, utils Suggests: rmarkdown, knitr, testthat, BiocStyle Enhances: celldex, future, SingleR, SummarizedExperiment, tricycle License: GPL-3 Package: scruff Version: 1.22.0 Depends: R (>= 4.0) Imports: data.table, GenomicAlignments, GenomicFeatures, txdbmaker, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment, Rsubread, parallelly Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE Package: scry Version: 1.16.0 Depends: R (>= 4.0), stats, methods Imports: DelayedArray, glmpca (>= 0.2.0), Matrix, SingleCellExperiment, SummarizedExperiment, BiocSingular Suggests: BiocGenerics, covr, DuoClustering2018, ggplot2, HDF5Array, knitr, markdown, rmarkdown, TENxPBMCData, testthat License: Artistic-2.0 Package: scShapes Version: 1.10.0 Depends: R (>= 4.1) Imports: Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS, emdbook, magrittr, utils Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 Package: scTensor Version: 2.14.0 Depends: R (>= 4.1.0) Imports: methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor (>= 1.1.5), ccTensor (>= 1.0.2), rTensor (>= 1.4.8), abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi (>= 1.29.2), grDevices, graphics, stats, utils, outliers, Category, meshr (>= 1.99.1), GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork, schex, ggplot2 Suggests: testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens, AnnotationHub License: Artistic-2.0 Package: scTGIF Version: 1.18.0 Depends: R (>= 3.6.0) Imports: GSEABase, Biobase, SingleCellExperiment, BiocStyle, plotly, tagcloud, rmarkdown, Rcpp, grDevices, graphics, utils, knitr, S4Vectors, SummarizedExperiment, RColorBrewer, nnTensor, methods, scales, msigdbr, schex, tibble, ggplot2, igraph Suggests: testthat License: Artistic-2.0 Package: scTHI Version: 1.16.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown, BiocStyle License: GPL-2 Package: scTreeViz Version: 1.10.0 Depends: R (>= 4.0), methods, epivizr, SummarizedExperiment Imports: data.table, S4Vectors, digest, Matrix, Rtsne, httr, igraph, clustree, scran, sys, epivizrData, epivizrServer, ggraph, scater, Seurat, SingleCellExperiment, ggplot2, stats, utils Suggests: knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb License: Artistic-2.0 Package: scuttle Version: 1.14.0 Depends: SingleCellExperiment Imports: methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, DelayedArray, DelayedMatrixStats, beachmat LinkingTo: Rcpp, beachmat Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat, scran License: GPL-3 Archs: x64 Package: SDAMS Version: 1.24.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL Package: sechm Version: 1.12.0 Depends: R (>= 4.0), SummarizedExperiment, ComplexHeatmap Imports: S4Vectors, seriation, circlize, methods, randomcoloR, stats, grid, grDevices, matrixStats Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 Package: segmenter Version: 1.10.0 Depends: R (>= 4.1) Imports: ChIPseeker, GenomicRanges, SummarizedExperiment, IRanges, S4Vectors, bamsignals, ComplexHeatmap, graphics, stats, utils, methods, chromhmmData Suggests: testthat, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz License: GPL-3 Package: segmentSeq Version: 2.38.0 Depends: R (>= 3.5.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel, GenomicRanges, ShortRead, stats Imports: Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils, abind Suggests: BiocStyle, BiocGenerics License: GPL-3 Package: selectKSigs Version: 1.16.0 Depends: R(>= 3.6) Imports: HiLDA, magrittr, gtools, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr License: GPL-3 Archs: x64 Package: SELEX Version: 1.36.0 Depends: rJava (>= 0.5-0), Biostrings (>= 2.26.0) Imports: stats, utils License: GPL (>= 2) Package: SemDist Version: 1.38.0 Depends: R (>= 3.1), AnnotationDbi, GO.db, annotate Suggests: GOSemSim License: GPL (>= 2) Package: semisup Version: 1.28.0 Depends: R (>= 3.0.0) Imports: VGAM Suggests: knitr, testthat, SummarizedExperiment License: GPL-3 Package: seq2pathway Version: 1.36.0 Depends: R (>= 3.6.2) Imports: nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data License: GPL-2 Package: seqArchR Version: 1.8.0 Depends: R (>= 4.2.0) Imports: utils, graphics, cvTools (>= 0.3.2), MASS, Matrix, methods, stats, cluster, matrixStats, fpc, cli, prettyunits, reshape2 (>= 1.4.3), reticulate (>= 1.22), BiocParallel, Biostrings, grDevices, ggplot2 (>= 3.1.1), ggseqlogo (>= 0.1) Suggests: cowplot, hopach (>= 2.42.0), BiocStyle, knitr (>= 1.22), rmarkdown (>= 1.12), testthat (>= 3.0.2), covr, vdiffr (>= 0.3.0) License: GPL-3 | file LICENSE Package: seqArchRplus Version: 1.4.0 Depends: R (>= 4.2), GenomicRanges, IRanges, S4Vectors Imports: BiocParallel, Biostrings, BSgenome, ChIPseeker, cli, clusterProfiler, cowplot, factoextra, GenomeInfoDb, ggplot2, ggimage, graphics, grDevices, gridExtra, heatmaps, magick, methods, RColorBrewer, scales, seqArchR, seqPattern, stats, utils Suggests: BSgenome.Dmelanogaster.UCSC.dm6, BiocStyle, CAGEr (>= 2.0.2), covr, knitr (>= 1.22), org.Dm.eg.db, pdftools, rmarkdown (>= 1.12), slickR, TxDb.Dmelanogaster.UCSC.dm6.ensGene, xfun License: GPL-3 Package: SeqArray Version: 1.44.0 Depends: R (>= 3.5.0), gdsfmt (>= 1.31.1) Imports: methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors LinkingTo: gdsfmt Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation License: GPL-3 Archs: x64 Package: seqCAT Version: 1.26.0 Depends: R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>= 1.20.3) Imports: dplyr (>= 0.5.0), GenomeInfoDb (>= 1.13.4), ggplot2 (>= 2.2.1), grid (>= 3.5.0), IRanges (>= 2.8.2), methods, rtracklayer, rlang, scales (>= 0.4.1), S4Vectors (>= 0.12.2), stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager License: MIT + file LICENCE Package: seqcombo Version: 1.26.0 Depends: R (>= 3.4.0) Imports: ggplot2, grid, igraph, utils, yulab.utils Suggests: emojifont, knitr, rmarkdown, prettydoc, tibble License: Artistic-2.0 Package: SeqGate Version: 1.14.0 Depends: S4Vectors, SummarizedExperiment, GenomicRanges Imports: stats, methods, BiocManager Suggests: testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown License: GPL (>= 2.0) Package: SeqGSEA Version: 1.44.0 Depends: Biobase, doParallel, DESeq2 Imports: methods, biomaRt Suggests: GenomicRanges License: GPL (>= 3) Package: seq.hotSPOT Version: 1.4.0 Depends: R (>= 3.5.0) Imports: R.utils, hash, stats, base, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 Package: seqLogo Version: 1.70.0 Depends: R (>= 4.2), methods, grid Imports: stats4, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat License: LGPL (>= 2) Package: seqPattern Version: 1.36.0 Depends: methods, R (>= 2.15.0) Imports: Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle Enhances: parallel License: GPL-3 Package: seqsetvis Version: 1.24.0 Depends: R (>= 3.6), ggplot2 Imports: cowplot, data.table, eulerr, GenomeInfoDb, GenomicAlignments, GenomicRanges, ggplotify, grDevices, grid, IRanges, limma, methods, pbapply, pbmcapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, scales, stats, UpSetR Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, knitr, rmarkdown, testthat License: MIT + file LICENSE Package: SeqSQC Version: 1.26.0 Depends: R (>= 3.4), ExperimentHub (>= 1.3.7), SNPRelate (>= 1.10.2) Imports: e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges, methods, plotly, RColorBrewer, reshape2, rmarkdown, S4Vectors, stats, utils Suggests: BiocStyle, knitr, testthat License: GPL-3 Package: seqTools Version: 1.38.0 Depends: methods,utils,zlibbioc LinkingTo: zlibbioc Suggests: RUnit, BiocGenerics License: Artistic-2.0 Archs: x64 Package: SeqVarTools Version: 1.42.0 Depends: SeqArray Imports: grDevices, graphics, stats, methods, Biobase, BiocGenerics, gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf, Matrix, data.table, Suggests: BiocStyle, RUnit, stringr License: GPL-3 Package: sesame Version: 1.22.2 Depends: R (>= 4.3.0), sesameData Imports: graphics, BiocParallel, utils, methods, stringr, readr, tibble, MASS, wheatmap (>= 0.2.0), GenomicRanges, IRanges, grid, preprocessCore, S4Vectors, ggplot2, BiocFileCache, GenomeInfoDb, stats, SummarizedExperiment, dplyr, reshape2 Suggests: scales, BiocManager, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals License: MIT + file LICENSE Package: SEtools Version: 1.18.0 Depends: R (>= 4.0), SummarizedExperiment, sechm Imports: BiocParallel, Matrix, DESeq2, S4Vectors, data.table, edgeR, openxlsx, pheatmap, stats, circlize, methods, sva Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: GPL Package: sevenbridges Version: 1.34.0 Depends: methods, utils, stats Imports: httr, jsonlite, yaml, objectProperties, stringr, S4Vectors, docopt, curl, uuid, data.table Suggests: knitr, rmarkdown, testthat, readr License: Apache License 2.0 | file LICENSE Package: sevenC Version: 1.24.0 Depends: R (>= 3.5), InteractionSet (>= 1.2.0) Imports: rtracklayer (>= 1.34.1), BiocGenerics (>= 0.22.0), GenomeInfoDb (>= 1.12.2), GenomicRanges (>= 1.28.5), IRanges (>= 2.10.3), S4Vectors (>= 0.14.4), readr (>= 1.1.0), purrr (>= 0.2.2), data.table (>= 1.10.4), boot (>= 1.3-20), methods (>= 3.4.1) Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr License: GPL-3 Package: SGSeq Version: 1.38.0 Depends: R (>= 4.0), IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), Rsamtools (>= 1.31.2), SummarizedExperiment, methods Imports: AnnotationDbi, BiocGenerics (>= 0.31.5), Biostrings (>= 2.47.6), GenomicAlignments (>= 1.15.7), GenomicFeatures (>= 1.31.5), GenomeInfoDb, RUnit, S4Vectors (>= 0.23.19), grDevices, graphics, igraph, parallel, rtracklayer (>= 1.39.7), stats Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown License: Artistic-2.0 Package: SharedObject Version: 1.18.0 Depends: R (>= 3.6.0) Imports: Rcpp, methods, stats, BiocGenerics LinkingTo: BH, Rcpp Suggests: testthat, parallel, knitr, rmarkdown, BiocStyle License: GPL-3 Archs: x64 Package: shinyepico Version: 1.12.0 Depends: R (>= 4.3.0) Imports: DT (>= 0.15.0), data.table (>= 1.13.0), doParallel (>= 1.0.0), dplyr (>= 1.0.9), foreach (>= 1.5.0), GenomicRanges (>= 1.38.0), ggplot2 (>= 3.3.0), gplots (>= 3.0.0), heatmaply (>= 1.1.0), limma (>= 3.42.0), minfi (>= 1.32.0), plotly (>= 4.9.2), reshape2 (>= 1.4.0), rlang (>= 1.0.2), rmarkdown (>= 2.3.0), rtracklayer (>= 1.46.0), shiny (>= 1.5.0), shinyWidgets (>= 0.5.0), shinycssloaders (>= 0.3.0), shinyjs (>= 1.1.0), shinythemes (>= 1.1.0), statmod (>= 1.4.0), tidyr (>= 1.2.0), zip (>= 2.1.0) Suggests: knitr (>= 1.30.0), mCSEA (>= 1.10.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICmanifest, testthat, minfiData, BiocStyle License: AGPL-3 + file LICENSE Package: shiny.gosling Version: 1.0.1 Imports: htmltools, jsonlite, rlang, shiny, shiny.react (== 0.3.0), fs, digest, rjson Suggests: config, covr, knitr, lintr, mockery (>= 0.4.3), rcmdcheck, rmarkdown, sessioninfo, spelling, testthat (>= 3.0.0), GenomicRanges, VariantAnnotation, StructuralVariantAnnotation, biovizBase, ggbio License: LGPL-3 Package: shinyMethyl Version: 1.40.0 Imports: Biobase, BiocGenerics, graphics, grDevices, htmltools, MatrixGenerics, methods, minfi, RColorBrewer, shiny, stats, utils Suggests: shinyMethylData, minfiData, BiocStyle, knitr, testthat License: Artistic-2.0 Package: ShortRead Version: 1.62.0 Depends: BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6) Imports: Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), pwalign, hwriter, methods, zlibbioc, lattice, latticeExtra, LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib, zlibbioc Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi, knitr License: Artistic-2.0 Archs: x64 Package: SIAMCAT Version: 2.8.0 Depends: R (>= 4.2.0), mlr3, phyloseq Imports: beanplot, glmnet, graphics, grDevices, grid, gridBase, gridExtra, LiblineaR, matrixStats, methods, pROC, PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo, progress, corrplot, lmerTest, mlr3learners, mlr3tuning, paradox, lgr Suggests: BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr License: GPL-3 Package: SigCheck Version: 2.36.0 Depends: R (>= 4.0.0), MLInterfaces, Biobase, e1071, BiocParallel, survival Imports: graphics, stats, utils, methods Suggests: BiocStyle, breastCancerNKI, qusage License: Artistic-2.0 Package: sigFeature Version: 1.22.0 Depends: R (>= 3.5.0) Imports: biocViews, nlme, e1071, openxlsx, pheatmap, RColorBrewer, Matrix, SparseM, graphics, stats, utils, SummarizedExperiment, BiocParallel, methods Suggests: RUnit, BiocGenerics, knitr, rmarkdown License: GPL (>= 2) Package: SigFuge Version: 1.42.0 Depends: R (>= 3.5.0), GenomicRanges Imports: ggplot2, matlab, reshape, sigclust Suggests: org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0), TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle License: GPL-3 Package: siggenes Version: 1.78.0 Depends: Biobase, multtest, splines, methods Imports: stats4, grDevices, graphics, stats, scrime (>= 1.2.5) Suggests: affy, annotate, genefilter, KernSmooth License: LGPL (>= 2) Package: sights Version: 1.30.0 Depends: R(>= 3.3) Imports: MASS(>= 7.3), qvalue(>= 2.2), ggplot2(>= 2.0), reshape2(>= 1.4), lattice(>= 0.2), stats(>= 3.3) Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx License: GPL-3 | file LICENSE Package: signatureSearch Version: 1.18.0 Depends: R(>= 4.2.0), Rcpp, SummarizedExperiment, org.Hs.eg.db Imports: AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array, magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue, stats, utils, reshape2, visNetwork, BiocParallel, fastmatch, reactome.db, Matrix, clusterProfiler, readr, DOSE, rhdf5, GSEABase, DelayedArray, BiocGenerics, tibble LinkingTo: Rcpp Suggests: knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT License: Artistic-2.0 Archs: x64 Package: signeR Version: 2.6.0 Depends: R (>= 3.0.2), VariantAnnotation, NMF Imports: BiocGenerics, Biostrings, class, grDevices, GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats, utils, PMCMRplus, parallel, pvclust, ppclust, clue, survival, maxstat, survivalAnalysis, future, VGAM, MASS, kknn, glmnet, e1071, randomForest, ada, future.apply, ggplot2, pROC, pheatmap, RColorBrewer, listenv, reshape2, scales, survminer, dplyr, ggpubr, cowplot, tibble, readr, shiny, shinydashboard, shinycssloaders, shinyWidgets, bsplus, DT, magrittr, tidyr, BiocFileCache, proxy, rtracklayer, BSgenome LinkingTo: Rcpp, RcppArmadillo (>= 0.7.100) Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, rmarkdown License: GPL-3 Archs: x64 Package: signifinder Version: 1.6.0 Depends: R (>= 4.3.0) Imports: AnnotationDbi, BiocGenerics, ComplexHeatmap, consensusOV, cowplot, DGEobj.utils, dplyr, ensembldb, ggplot2, ggridges, GSVA, IRanges, magrittr, matrixStats, maxstat, methods, openair, org.Hs.eg.db, patchwork, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, sparrow, SpatialExperiment, stats, SummarizedExperiment, survival, survminer, viridis Suggests: BiocStyle, edgeR, grid, kableExtra, knitr, limma, testthat (>= 3.0.0) License: AGPL-3 Package: SigsPack Version: 1.18.0 Depends: R (>= 3.6) Imports: quadprog (>= 1.5-5), methods, Biobase, BSgenome (>= 1.46.0), VariantAnnotation (>= 1.24.5), Biostrings, GenomeInfoDb, GenomicRanges, rtracklayer, SummarizedExperiment, graphics, stats, utils Suggests: IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown License: GPL-3 Package: sigsquared Version: 1.36.0 Depends: R (>= 3.2.0), methods Imports: Biobase, survival Suggests: RUnit, BiocGenerics License: GPL-3 Package: SIM Version: 1.74.0 Depends: R (>= 3.5), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt, RColorBrewer License: GPL (>= 2) Archs: x64 Package: SIMAT Version: 1.36.0 Depends: R (>= 3.5.0), Rcpp (>= 0.11.3) Imports: mzR, ggplot2, grid, reshape2, grDevices, stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 Package: SimBu Version: 1.6.0 Imports: basilisk, BiocParallel, data.table, dplyr, ggplot2, tools, Matrix (>= 1.3.3), methods, phyloseq, proxyC, RColorBrewer, RCurl, reticulate, sparseMatrixStats, SummarizedExperiment, tidyr Suggests: curl, knitr, matrixStats, rmarkdown, Seurat (>= 5.0.0), SeuratObject (>= 5.0.0), testthat (>= 3.0.0) License: GPL-3 + file LICENSE Package: SIMD Version: 1.22.0 Depends: R (>= 3.5.0) Imports: edgeR, statmod, methylMnM, stats, utils Suggests: BiocStyle, knitr,rmarkdown License: GPL-3 Archs: x64 Package: SimFFPE Version: 1.16.0 Depends: Biostrings Imports: dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods Suggests: BiocStyle License: LGPL-3 Package: similaRpeak Version: 1.36.0 Depends: R6 (>= 2.0) Imports: stats Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle License: Artistic-2.0 Package: SIMLR Version: 1.30.0 Depends: R (>= 4.1.0), Imports: parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy, RSpectra LinkingTo: Rcpp Suggests: BiocGenerics, BiocStyle, testthat, knitr, igraph License: file LICENSE Archs: x64 Package: simona Version: 1.2.0 Depends: R (>= 4.1.0) Imports: methods, Rcpp, matrixStats, GetoptLong, grid, GlobalOptions, igraph, Polychrome, S4Vectors, xml2 (>= 1.3.3), circlize, ComplexHeatmap, grDevices, stats, utils, shiny LinkingTo: Rcpp Suggests: knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png, InteractiveComplexHeatmap, UniProtKeywords, simplifyEnrichment, AnnotationHub, jsonlite License: MIT + file LICENSE Archs: x64 Package: simPIC Version: 1.0.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: BiocGenerics, checkmate (>= 2.0.0), fitdistrplus, matrixStats, Matrix, stats, SummarizedExperiment, actuar, rlang, S4Vectors, methods, scales, scuttle Suggests: ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 Package: simpleSeg Version: 1.6.1 Depends: R (>= 3.5.0) Imports: BiocParallel, EBImage, terra, stats, spatstat.geom, S4Vectors, grDevices, SummarizedExperiment, methods, cytomapper Suggests: BiocStyle, testthat (>= 3.0.0), knitr, ggplot2 License: GPL-3 Package: simplifyEnrichment Version: 1.14.0 Depends: R (>= 3.6.0), BiocGenerics, grid Imports: GOSemSim, ComplexHeatmap (>= 2.7.4), circlize, GetoptLong, digest, tm, GO.db, org.Hs.eg.db, AnnotationDbi, slam, methods, clue, grDevices, graphics, stats, utils, proxyC, Matrix, cluster (>= 1.14.2), colorspace, GlobalOptions (>= 0.1.0) Suggests: knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, clusterProfiler, msigdbr, DOSE, DO.db, reactome.db, flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11), shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter, gridtext, fpc License: MIT + file LICENSE Package: sincell Version: 1.36.0 Depends: R (>= 3.0.2), igraph Imports: Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2, reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster, statmod LinkingTo: Rcpp Suggests: BiocStyle, knitr, biomaRt, stringr, monocle License: GPL (>= 2) Archs: x64 Package: single Version: 1.8.0 Depends: R (>= 4.0) Imports: Biostrings, BiocGenerics, dplyr, GenomicAlignments,IRanges, methods, reshape2, rlang, Rsamtools, stats, stringr, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE Package: SingleCellExperiment Version: 1.26.0 Depends: SummarizedExperiment Imports: methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>= 2.9.1), Rtsne License: GPL-3 Package: SingleCellSignalR Version: 1.16.0 Depends: R (>= 4.0) Imports: BiocManager, circlize, limma, igraph, gplots, grDevices, edgeR, data.table, pheatmap, stats, Rtsne, graphics, stringr, foreach, multtest, scran, utils, Suggests: knitr, rmarkdown License: GPL-3 Package: singleCellTK Version: 2.14.0 Depends: R (>= 4.0), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase Imports: ape, anndata, AnnotationHub, batchelor, BiocParallel, celldex, colourpicker, colorspace, cowplot, cluster, ComplexHeatmap, data.table, DelayedMatrixStats, DESeq2, dplyr, DT, ExperimentHub, ensembldb, fields, ggplot2, ggplotify, ggrepel, ggtree, gridExtra, GSVA (>= 1.50.0), GSVAdata, igraph, KernSmooth, limma, MAST, Matrix (>= 1.6-1), matrixStats, methods, msigdbr, multtest, plotly, plyr, ROCR, Rtsne, S4Vectors, scater, scMerge (>= 1.2.0), scran, Seurat (>= 3.1.3), shiny, shinyjs, SingleR, SoupX, sva, reshape2, shinyalert, circlize, enrichR (>= 3.2), celda, shinycssloaders, DropletUtils, scds (>= 1.2.0), reticulate (>= 1.14), tools, tximport, eds, withr, GSEABase, R.utils, zinbwave, scRNAseq (>= 2.0.2), TENxPBMCData, yaml, rmarkdown, magrittr, scDblFinder, metap, VAM (>= 0.5.3), tibble, rlang, TSCAN, TrajectoryUtils, scuttle, utils, stats, zellkonverter Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, spelling, org.Mm.eg.db, stringr, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics, RColorBrewer, fastmap (>= 1.1.0), harmony, SeuratObject, optparse License: MIT + file LICENSE Package: SingleMoleculeFootprinting Version: 1.12.0 Depends: R (>= 4.1.0) Imports: BiocGenerics, Biostrings, BSgenome, GenomeInfoDb, GenomicRanges, data.table, grDevices, plyr, IRanges, RColorBrewer, stats, QuasR Suggests: BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, parallel, rmarkdown, readr, SingleMoleculeFootprintingData, testthat (>= 3.0.0) License: GPL-3 Package: SingleR Version: 2.6.0 Depends: SummarizedExperiment Imports: methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocSingular, stats, utils, Rcpp, beachmat, parallel LinkingTo: Rcpp, beachmat, BiocNeighbors Suggests: testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scater, scran, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex License: GPL-3 + file LICENSE Archs: x64 Package: singscore Version: 1.24.0 Depends: R (>= 3.6) Imports: methods, stats, graphics, ggplot2, grDevices, ggrepel, GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR, RColorBrewer, Biobase, BiocParallel, SummarizedExperiment, matrixStats, reshape2, S4Vectors Suggests: pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr License: GPL-3 Package: SiPSiC Version: 1.4.0 Depends: Matrix, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle License: file LICENSE Package: sitadela Version: 1.12.0 Depends: R (>= 4.1.0) Imports: Biobase, BiocGenerics, biomaRt, Biostrings, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, methods, parallel, Rsamtools, RSQLite, rtracklayer, S4Vectors, tools, txdbmaker, utils Suggests: BiocStyle, BSgenome, knitr, rmarkdown, RMySQL, RUnit License: Artistic-2.0 Package: sitePath Version: 1.20.0 Depends: R (>= 4.1) Imports: RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree, graphics, grDevices, gridExtra, methods, parallel, seqinr, stats, tidytree, utils LinkingTo: Rcpp Suggests: BiocStyle, devtools, knitr, magick, rmarkdown, testthat License: MIT + file LICENSE Archs: x64 Package: sizepower Version: 1.74.0 Depends: stats License: LGPL Package: sketchR Version: 1.0.0 Imports: basilisk, Biobase, DelayedArray, dplyr, ggplot2, methods, reticulate, rlang, scales, stats Suggests: rmarkdown, knitr, testthat (>= 3.0.0), TENxPBMCData, scuttle, scran, scater, SingleR, celldex, cowplot, SummarizedExperiment, beachmat.hdf5, BiocStyle, BiocManager, SingleCellExperiment License: MIT + file LICENSE Package: skewr Version: 1.36.0 Depends: R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest Imports: minfi, S4Vectors (>= 0.19.1), RColorBrewer Suggests: GEOquery, knitr, minfiData License: GPL-2 Package: slalom Version: 1.26.0 Depends: R (>= 4.0) Imports: Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase, methods, rsvd, SingleCellExperiment, SummarizedExperiment, stats LinkingTo: Rcpp, RcppArmadillo, BH Suggests: BiocStyle, knitr, rhdf5, rmarkdown, scater, testthat License: GPL-2 Archs: x64 Package: slingshot Version: 2.12.0 Depends: R (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils Imports: graphics, grDevices, igraph, matrixStats, methods, S4Vectors, SingleCellExperiment, SummarizedExperiment Suggests: BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr License: Artistic-2.0 Package: SLqPCR Version: 1.70.0 Depends: R(>= 2.4.0) Imports: stats Suggests: RColorBrewer License: GPL (>= 2) Package: SMAD Version: 1.20.0 Depends: R (>= 3.6.0), RcppAlgos Imports: magrittr (>= 1.5), dplyr, stats, tidyr, utils, Rcpp (>= 1.0.0) LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE Archs: x64 Package: SMAP Version: 1.68.0 Depends: R (>= 2.10), methods License: GPL-2 Archs: x64 Package: smartid Version: 1.0.2 Depends: R (>= 4.4) Imports: dplyr, ggplot2, graphics, Matrix, mclust, methods, mixtools, sparseMatrixStats, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, dbscan, ggpubr, knitr, rmarkdown, scater, splatter, testthat (>= 3.0.0), tidytext, UpSetR License: MIT + file LICENSE Package: SMITE Version: 1.32.0 Depends: R (>= 3.5), GenomicRanges Imports: scales, plyr, Hmisc, AnnotationDbi, org.Hs.eg.db, ggplot2, reactome.db, KEGGREST, BioNet, goseq, methods, IRanges, igraph, Biobase,tools, S4Vectors, geneLenDataBase, grDevices, graphics, stats, utils Suggests: knitr, rmarkdown License: GPL (>= 2) Package: smoothclust Version: 1.0.0 Depends: R (>= 4.4.0) Imports: SpatialExperiment, SummarizedExperiment, sparseMatrixStats, spdep, methods, utils Suggests: BiocStyle, knitr, STexampleData, scuttle, scran, scater, ggspavis, testthat License: MIT + file LICENSE Package: SNAGEE Version: 1.44.0 Depends: R (>= 2.6.0), SNAGEEdata Suggests: ALL, hgu95av2.db Enhances: parallel License: Artistic-2.0 Package: snapcount Version: 1.16.0 Depends: R (>= 4.0.0) Imports: R6, httr, rlang, purrr, jsonlite, assertthat, data.table, Matrix, magrittr, methods, stringr, stats, IRanges, GenomicRanges, SummarizedExperiment Suggests: BiocManager, bit64, covr, knitcitations, knitr (>= 1.6), devtools, BiocStyle (>= 2.5.19), rmarkdown (>= 0.9.5), testthat (>= 2.1.0) License: MIT + file LICENSE Package: snifter Version: 1.14.0 Depends: R (>= 4.0.0) Imports: basilisk, reticulate, irlba, stats, assertthat Suggests: knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0) License: GPL-3 Package: snm Version: 1.52.0 Depends: R (>= 2.12.0) Imports: corpcor, lme4 (>= 1.0), splines License: LGPL Package: SNPhood Version: 1.34.0 Depends: R (>= 3.5.0), GenomicRanges, Rsamtools, data.table, checkmate Imports: DESeq2, cluster, ggplot2, lattice, GenomeInfoDb (>= 1.34.8), BiocParallel, VariantAnnotation, BiocGenerics, IRanges, methods, SummarizedExperiment, RColorBrewer, Biostrings, grDevices, gridExtra, stats, grid, utils, reshape2, scales, S4Vectors Suggests: BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot License: LGPL (>= 3) Package: SNPRelate Version: 1.38.0 Depends: R (>= 2.15), gdsfmt (>= 1.8.3) Imports: methods LinkingTo: gdsfmt Suggests: parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS, BiocGenerics Enhances: SeqArray (>= 1.12.0) License: GPL-3 Archs: x64 Package: snpStats Version: 1.54.0 Depends: R(>= 2.10.0), survival, Matrix, methods Imports: graphics, grDevices, stats, utils, BiocGenerics, zlibbioc Suggests: hexbin License: GPL-3 Archs: x64 Package: soGGi Version: 1.36.0 Depends: R (>= 3.5.0), BiocGenerics, SummarizedExperiment Imports: methods, reshape2, ggplot2, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, preprocessCore, chipseq, BiocParallel Suggests: testthat, BiocStyle, knitr License: GPL (>= 3) Package: SomaticSignatures Version: 2.40.0 Depends: R (>= 3.5.0), VariantAnnotation, GenomicRanges, NMF Imports: S4Vectors, IRanges, GenomeInfoDb, Biostrings, ggplot2, ggbio, reshape2, NMF, pcaMethods, Biobase, methods, proxy Suggests: testthat, knitr, parallel, BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations, ggdendro, fastICA, sva License: MIT + file LICENSE Package: SOMNiBUS Version: 1.12.0 Depends: R (>= 4.1.0) Imports: Matrix, mgcv, stats, VGAM, IRanges, GenomeInfoDb, GenomicRanges, rtracklayer, S4Vectors, BiocManager, annotatr, yaml, utils, bsseq, reshape2, data.table, ggplot2, tidyr, Suggests: BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, License: MIT + file LICENSE Package: SpaceMarkers Version: 1.0.0 Depends: R (>= 4.4.0) Imports: matrixStats, matrixTests, rstatix, spatstat.explore, spatstat.geom, ape, hdf5r, jsonlite, Matrix, qvalue, stats, utils, methods Suggests: data.table, devtools, dplyr, ggplot2, hrbrthemes, knitr, RColorBrewer, cowplot, readbitmap, rjson, rmarkdown, BiocStyle, testthat (>= 3.0.0), viridis, CoGAPS License: MIT + file LICENSE Package: SpacePAC Version: 1.42.0 Depends: R(>= 2.15),iPAC Suggests: RUnit, BiocGenerics, rgl License: GPL-2 Package: Spaniel Version: 1.18.0 Depends: R (>= 4.0) Imports: Seurat, SingleCellExperiment, SummarizedExperiment, dplyr, methods, ggplot2, scater (>= 1.13), scran, igraph, shiny, jpeg, magrittr, utils, S4Vectors, DropletUtils, jsonlite, png Suggests: knitr, rmarkdown, testthat, devtools License: MIT + file LICENSE Package: sparrow Version: 1.10.1 Depends: R (>= 4.0) Imports: babelgene (>= 21.4), BiocGenerics, BiocParallel, BiocSet, checkmate, circlize, ComplexHeatmap (>= 2.0), data.table (>= 1.10.4), DelayedMatrixStats, edgeR (>= 3.18.1), ggplot2 (>= 2.2.0), graphics, grDevices, GSEABase, irlba, limma, Matrix, methods, plotly (>= 4.9.0), stats, utils, viridis Suggests: AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle, DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin, magrittr, matrixStats, msigdbr (>= 7.4.1), KernSmooth, knitr, PANTHER.db (>= 1.0.3), R.utils, reactome.db, rmarkdown, SummarizedExperiment, statmod, stringr, testthat, webshot License: MIT + file LICENSE Package: SparseArray Version: 1.4.8 Depends: R (>= 4.3.0), methods, Matrix, BiocGenerics (>= 0.43.1), MatrixGenerics (>= 1.11.1), S4Vectors, S4Arrays (>= 1.4.1) Imports: utils, stats, matrixStats, IRanges, XVector LinkingTo: S4Vectors, IRanges, XVector Suggests: DelayedArray, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 Archs: x64 Package: sparseDOSSA Version: 1.28.0 Imports: stats, utils, optparse, MASS, tmvtnorm (>= 1.4.10), MCMCpack Suggests: knitr, BiocStyle, BiocGenerics, rmarkdown License: MIT + file LICENSE Package: sparseMatrixStats Version: 1.16.0 Depends: MatrixGenerics (>= 1.5.3) Imports: Rcpp, Matrix, matrixStats (>= 0.60.0), methods LinkingTo: Rcpp Suggests: testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle License: MIT + file LICENSE Archs: x64 Package: sparsenetgls Version: 1.22.0 Depends: R (>= 4.0.0), Matrix, MASS Imports: methods, glmnet, huge, stats, graphics, utils Suggests: testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) License: GPL-3 Package: SparseSignatures Version: 2.14.0 Depends: R (>= 4.1.0), NMF Imports: nnlasso, nnls, parallel, data.table, Biostrings, GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2, gridExtra, reshape2 Suggests: BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5, BiocStyle, testthat, knitr, License: file LICENSE Package: spaSim Version: 1.6.0 Depends: R (>= 4.2.0) Imports: ggplot2, methods, stats, dplyr, spatstat.geom, spatstat.random, SpatialExperiment, SummarizedExperiment, RANN Suggests: RefManageR, BiocStyle, knitr, testthat (>= 3.0.0), sessioninfo, rmarkdown, markdown License: Artistic-2.0 Package: SpatialCPie Version: 1.20.0 Depends: R (>= 3.6) Imports: colorspace (>= 1.3-2), data.table (>= 1.12.2), digest (>= 0.6.21), dplyr (>= 0.7.6), ggforce (>= 0.3.0), ggiraph (>= 0.5.0), ggplot2 (>= 3.0.0), ggrepel (>= 0.8.0), grid (>= 3.5.1), igraph (>= 1.2.2), lpSolve (>= 5.6.13), methods (>= 3.5.0), purrr (>= 0.2.5), readr (>= 1.1.1), rlang (>= 0.2.2), shiny (>= 1.1.0), shinycssloaders (>= 0.2.0), shinyjs (>= 1.0), shinyWidgets (>= 0.4.8), stats (>= 3.6.0), SummarizedExperiment (>= 1.10.1), tibble (>= 1.4.2), tidyr (>= 0.8.1), tidyselect (>= 0.2.4), tools (>= 3.6.0), utils (>= 3.5.0), zeallot (>= 0.1.0) Suggests: BiocStyle (>= 2.8.2), jpeg (>= 0.1-8), knitr (>= 1.20), rmarkdown (>= 1.10), testthat (>= 2.0.0) License: MIT + file LICENSE Package: spatialDE Version: 1.10.0 Depends: R (>= 4.3) Imports: reticulate, basilisk (>= 1.9.10), checkmate, stats, SpatialExperiment, methods, SummarizedExperiment, Matrix, ggplot2, ggrepel, scales, gridExtra Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE Package: SpatialDecon Version: 1.14.0 Depends: R (>= 4.0.0) Imports: grDevices, stats, utils, graphics, SeuratObject, Biobase, GeomxTools, repmis, methods, Matrix, logNormReg (>= 0.4) Suggests: testthat, knitr, rmarkdown, qpdf, Seurat License: MIT + file LICENSE Package: SpatialExperiment Version: 1.14.0 Depends: methods, SingleCellExperiment Imports: rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, BiocGenerics, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils License: GPL-3 Package: spatialHeatmap Version: 2.10.1 Depends: R (>= 3.5.0) Imports: data.table, dplyr, edgeR, genefilter, ggplot2, grImport, grid, gridExtra, gplots, igraph, methods, Matrix, rsvg, shiny, grDevices, graphics, ggplotify, parallel, reshape2, scater, scuttle, scran, stats, SummarizedExperiment, SingleCellExperiment, shinydashboard, S4Vectors, spsComps (>= 0.3.3.0), tibble, utils, xml2 Suggests: AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, dendextend, DT, dynamicTreeCut, flashClust, ggdendro, HDF5Array, htmltools, htmlwidgets, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db, org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, plotly, rmarkdown, rols, rappdirs, RUnit, Rtsne, rhdf5, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, xlsx, yaml License: Artistic-2.0 Package: SpatialOmicsOverlay Version: 1.4.0 Depends: R (>= 4.1.0) Imports: S4Vectors, Biobase, base64enc, EBImage, ggplot2, XML, scattermore, dplyr, pbapply, data.table, readxl, magick, grDevices, stringr, plotrix, GeomxTools, BiocFileCache, stats, utils, methods, ggtext, tools, RBioFormats Suggests: knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr, sf License: MIT Package: spatzie Version: 1.10.0 Depends: R (>= 4.3) Imports: BiocGenerics, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicInteractions, GenomicRanges, ggplot2, IRanges, MatrixGenerics, matrixStats, motifmatchr, S4Vectors, stats, SummarizedExperiment, TFBSTools, utils Suggests: BiocManager, Biostrings, knitr, pheatmap, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene License: GPL-3 Package: speckle Version: 1.4.0 Depends: R (>= 4.2.0) Imports: limma, edgeR, SingleCellExperiment, Seurat, ggplot2, methods, stats, grDevices, graphics Suggests: BiocStyle, knitr, rmarkdown, statmod, CellBench, scater, patchwork, jsonlite, vdiffr, testthat (>= 3.0.0) License: GPL-3 Package: specL Version: 1.38.0 Depends: R (>= 4.1), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.7), RSQLite (>= 1.1), seqinr (>= 3.3) Suggests: BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4) License: GPL-3 Package: SpeCond Version: 1.58.0 Depends: R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13), fields, hwriter (>= 1.1), RColorBrewer, methods License: LGPL (>= 2) Package: Spectra Version: 1.14.1 Depends: R (>= 4.0.0), S4Vectors, BiocParallel, ProtGenerics (>= 1.35.4) Imports: methods, IRanges, MsCoreUtils (>= 1.7.5), graphics, grDevices, stats, tools, utils, fs, BiocGenerics, MetaboCoreUtils Suggests: testthat, knitr (>= 1.1.0), msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0), rmarkdown, vdiffr (>= 1.0.0), msentropy, patrick License: Artistic-2.0 Package: SpectralTAD Version: 1.20.0 Depends: R (>= 3.6) Imports: dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel, magrittr, HiCcompare, GenomicRanges, utils Suggests: BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr License: MIT + file LICENSE Package: SPEM Version: 1.44.0 Depends: R (>= 2.15.1), Rsolnp, Biobase, methods License: GPL-2 Package: SPIA Version: 2.56.0 Depends: R (>= 2.14.0), graphics, KEGGgraph Imports: graphics Suggests: graph, Rgraphviz, hgu133plus2.db License: file LICENSE License_restricts_use: yes Package: SPIAT Version: 1.6.1 Depends: R (>= 4.2.0), SpatialExperiment (>= 1.8.0) Imports: apcluster (>= 1.4.7), ggplot2 (>= 3.2.1), gridExtra (>= 2.3), gtools (>= 3.8.1), reshape2 (>= 1.4.3), dplyr (>= 0.8.3), RANN (>= 2.6.1), pracma (>= 2.2.5), dbscan (>= 1.1-5), mmand (>= 1.5.4), tibble (>= 2.1.3), grDevices, stats, utils, vroom, dittoSeq, spatstat.geom, methods, spatstat.explore, raster, sp, SummarizedExperiment, rlang Suggests: BiocStyle, plotly (>= 4.9.0), knitr, rmarkdown, pkgdown, testthat, graphics, alphahull, Rtsne, umap, ComplexHeatmap, elsa License: Artistic-2.0 + file LICENSE Package: spicyR Version: 1.16.1 Depends: R (>= 4.1) Imports: ggplot2, concaveman, BiocParallel, spatstat.explore, spatstat.geom, lmerTest, S4Vectors, methods, pheatmap, rlang, grDevices, stats, data.table, dplyr, tidyr, scam, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, ggforce, ClassifyR, tibble, magrittr, cli Suggests: BiocStyle, knitr, rmarkdown, pkgdown, imcRtools, testthat (>= 3.0.0) License: GPL (>= 2) Package: spikeLI Version: 2.64.0 Imports: graphics, grDevices, stats, utils License: GPL-2 Package: spiky Version: 1.10.0 Depends: Rsamtools, GenomicRanges, R (>= 3.6.0) Imports: stats, scales, bamlss, methods, tools, IRanges, Biostrings, GenomicAlignments, BlandAltmanLeh, GenomeInfoDb, BSgenome, S4Vectors, graphics, ggplot2, utils Suggests: covr, testthat, rmarkdown, markdown, knitr, devtools, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager License: GPL-2 Package: spillR Version: 1.0.0 Depends: R (>= 4.3.0), SummarizedExperiment, CATALYST Imports: dplyr, tibble, tidyselect, stats, ggplot2, tidyr, spatstat.geom, S4Vectors, parallel Suggests: knitr, rmarkdown, cowplot, testthat (>= 3.0.0), BiocStyle, hexbin License: LGPL-3 Package: spkTools Version: 1.60.0 Depends: R (>= 2.7.0), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), graphics, grDevices, gtools, methods, RColorBrewer, stats, utils Suggests: xtable License: GPL (>= 2) Package: splatter Version: 1.28.0 Depends: R (>= 4.0), SingleCellExperiment Imports: BiocGenerics, BiocParallel, checkmate (>= 2.0.0), crayon, edgeR, fitdistrplus, grDevices, locfit, matrixStats, methods, rlang, S4Vectors, scuttle, stats, SummarizedExperiment, utils, withr Suggests: BASiCS (>= 1.7.10), BiocManager, BiocSingular, BiocStyle, Biostrings, covr, cowplot, GenomeInfoDb, GenomicRanges, ggplot2 (>= 3.4.0), IRanges, igraph, knitr, limSolve, lme4, magick, mfa, phenopath, progress, preprocessCore, pscl, rmarkdown, scales, scater (>= 1.15.16), scDD, scran, SparseDC, spelling, testthat, VariantAnnotation, zinbwave, License: GPL-3 + file LICENSE Package: SpliceWiz Version: 1.6.0 Depends: R (>= 3.5.0), NxtIRFdata Imports: ompBAM, methods, stats, utils, tools, parallel, scales, magrittr, Rcpp (>= 1.0.5), data.table, fst, ggplot2, AnnotationHub, BiocFileCache, BiocGenerics, BiocParallel, Biostrings, BSgenome, DelayedArray, DelayedMatrixStats, genefilter, GenomeInfoDb, GenomicRanges, HDF5Array, htmltools, IRanges, patchwork, pheatmap, progress, plotly, R.utils, rhdf5, rtracklayer, SummarizedExperiment, S4Vectors, shiny, shinyFiles, shinyWidgets, shinydashboard, stringi, rhandsontable, DT, grDevices, heatmaply, matrixStats, RColorBrewer, rvest LinkingTo: ompBAM, Rcpp, zlibbioc, RcppProgress Suggests: knitr, rmarkdown, crayon, splines, testthat (>= 3.0.0), DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, AnnotationDbi, fgsea, Rsubread License: MIT + file LICENSE Archs: x64 Package: SplicingFactory Version: 1.12.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, methods, stats Suggests: testthat, knitr, rmarkdown, ggplot2, tidyr License: GPL-3 + file LICENSE Package: SplicingGraphs Version: 1.44.0 Depends: GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22), Rgraphviz (>= 2.3.7) Imports: methods, utils, graphics, igraph, BiocGenerics, S4Vectors (>= 0.17.5), BiocParallel, IRanges (>= 2.21.2), GenomeInfoDb, GenomicRanges (>= 1.23.21), Rsamtools, graph Suggests: igraph, Gviz, txdbmaker, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit License: Artistic-2.0 Package: splineTimeR Version: 1.32.0 Depends: R (>= 3.3), Biobase, igraph, limma, GSEABase, gtools, splines, GeneNet (>= 1.2.13), longitudinal (>= 1.1.12), FIs Suggests: knitr License: GPL-3 Package: SPLINTER Version: 1.30.0 Depends: R (>= 3.6.0), grDevices, stats Imports: graphics, ggplot2, seqLogo, Biostrings, pwalign, biomaRt, GenomicAlignments, GenomicRanges, GenomicFeatures, Gviz, IRanges, S4Vectors, GenomeInfoDb, utils, plyr,stringr, methods, BSgenome.Mmusculus.UCSC.mm9, googleVis Suggests: txdbmaker, BiocStyle, knitr, rmarkdown License: GPL-2 Package: splots Version: 1.70.0 Imports: grid, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown, assertthat, HD2013SGI, dplyr, ggplot2 License: LGPL Package: SPONGE Version: 1.26.0 Depends: R (>= 3.6) Imports: Biobase, stats, ppcor, logging, foreach, doRNG, data.table, MASS, expm, gRbase, glmnet, igraph, iterators, tidyverse, caret, dplyr, biomaRt, randomForest, ggridges, cvms, miRBaseConverter, ComplexHeatmap, ggplot2, MetBrewer, rlang, tnet, ggpubr, stringr, tidyr Suggests: testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra, digest, doParallel, bigmemory, GSVA License: GPL (>= 3) Package: spoon Version: 1.0.0 Depends: R (>= 4.4) Imports: SpatialExperiment, BRISC, nnSVG, BiocParallel, Matrix, methods, SummarizedExperiment, stats, utils, scuttle Suggests: testthat, STexampleData, knitr License: MIT + file LICENSE Package: SpotClean Version: 1.6.1 Depends: R (>= 4.2.0), Imports: stats, methods, utils, dplyr, S4Vectors, SummarizedExperiment, SpatialExperiment, Matrix, rhdf5, ggplot2, grid, readbitmap, rjson, tibble, viridis, grDevices, RColorBrewer, Seurat, rlang Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils, spelling License: GPL-3 Package: SPOTlight Version: 1.8.0 Depends: R (>= 4.1) Imports: ggplot2, NMF, Matrix, matrixStats, nnls, SingleCellExperiment, sparseMatrixStats, stats Suggests: BiocStyle, colorBlindness, DelayedArray, DropletUtils, ExperimentHub, ggcorrplot, grDevices, grid, igraph, jpeg, knitr, methods, png, rmarkdown, scater, scatterpie, scran, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat License: GPL-3 Package: SpotSweeper Version: 1.0.0 Depends: R (>= 4.3.0) Imports: SpatialExperiment, SummarizedExperiment, BiocNeighbors, SingleCellExperiment, stats, escheR, MASS, ggplot2, spatialEco, grDevices Suggests: knitr, BiocStyle, rmarkdown, scuttle, STexampleData, ggpubr, testthat (>= 3.0.0) License: MIT + file LICENSE Package: spqn Version: 1.16.0 Depends: R (>= 4.0), ggplot2, ggridges, SummarizedExperiment, BiocGenerics Imports: graphics, stats, utils, matrixStats Suggests: BiocStyle, knitr, rmarkdown, tools, spqnData (>= 0.99.3), RUnit License: Artistic-2.0 Package: SPsimSeq Version: 1.14.0 Depends: R (>= 4.0) Imports: stats, methods, SingleCellExperiment, fitdistrplus, graphics, edgeR, Hmisc, WGCNA, limma, mvtnorm, phyloseq, utils Suggests: knitr, rmarkdown, LSD, testthat, BiocStyle License: GPL-2 Package: SQLDataFrame Version: 1.18.0 Depends: DelayedArray, S4Vectors Imports: stats, utils, methods, BiocGenerics, RSQLite, duckdb, DBI Suggests: knitr, rmarkdown, BiocStyle, testthat Package: SQUADD Version: 1.54.0 Depends: R (>= 2.11.0) Imports: graphics, grDevices, methods, RColorBrewer, stats, utils License: GPL (>= 2) Package: sRACIPE Version: 1.20.0 Depends: R (>= 3.6.0),SummarizedExperiment, methods, Rcpp Imports: ggplot2, reshape2, MASS, RColorBrewer, gridExtra,visNetwork, gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices, stats, utils, graphics LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown, tinytest, doFuture License: MIT + file LICENSE Archs: x64 Package: SRAdb Version: 1.66.0 Depends: RSQLite, graph, RCurl Imports: GEOquery Suggests: Rgraphviz License: Artistic-2.0 Package: srnadiff Version: 1.24.0 Depends: R (>= 3.6) Imports: Rcpp (>= 0.12.8), stats, methods, devtools, S4Vectors, GenomeInfoDb, rtracklayer, SummarizedExperiment, IRanges, GenomicRanges, DESeq2, edgeR, Rsamtools, GenomicFeatures, GenomicAlignments, grDevices, Gviz, BiocParallel, BiocManager, BiocStyle LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocManager, BiocStyle License: GPL-3 Archs: x64 Package: sscu Version: 2.34.0 Depends: R (>= 3.3) Imports: Biostrings (>= 2.36.4), seqinr (>= 3.1-3), BiocGenerics (>= 0.16.1) Suggests: knitr, rmarkdown License: GPL (>= 2) Package: sSeq Version: 1.42.0 Depends: R (>= 3.0), caTools, RColorBrewer License: GPL (>= 3) Package: ssize Version: 1.78.0 Depends: gdata, xtable License: LGPL Package: sSNAPPY Version: 1.8.0 Depends: R (>= 4.3.0), ggplot2 Imports: dplyr (>= 1.1), magrittr, rlang, stats, graphite, tibble, ggraph, igraph, reshape2, org.Hs.eg.db, SummarizedExperiment, edgeR, methods, ggforce, pheatmap, utils, stringr, gtools, tidyr Suggests: BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools, knitr, pander, patchwork, rmarkdown, spelling, testthat (>= 3.0.0), tidyverse License: GPL-3 Package: ssPATHS Version: 1.18.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: ROCR, dml, MESS Suggests: ggplot2, testthat (>= 2.1.0) License: MIT + file LICENSE Package: ssrch Version: 1.20.0 Depends: R (>= 3.6), methods Imports: shiny, DT, utils Suggests: knitr, testthat, rmarkdown, BiocStyle License: Artistic-2.0 Package: ssviz Version: 1.38.0 Depends: R (>= 3.5.0), methods, Rsamtools, Biostrings, reshape, ggplot2, RColorBrewer, stats Suggests: knitr License: GPL-2 Package: stageR Version: 1.26.0 Depends: R (>= 3.4), SummarizedExperiment Imports: methods, stats Suggests: knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma, DEXSeq, testthat License: GNU General Public License version 3 Package: standR Version: 1.8.0 Depends: R (>= 4.1) Imports: dplyr, SpatialExperiment (>= 1.5.2), SummarizedExperiment, SingleCellExperiment, edgeR, rlang, readr, tibble, ggplot2, tidyr, ruv, limma, patchwork, S4Vectors, Biobase, BiocGenerics, grDevices, stats, methods, ggalluvial, mclustcomp, RUVSeq Suggests: knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr, ggrepel, cluster, testthat (>= 3.0.0) License: MIT + file LICENSE Package: staRank Version: 1.46.0 Depends: methods, cellHTS2, R (>= 2.10) License: GPL Package: STATegRa Version: 1.40.0 Depends: R (>= 2.10) Imports: Biobase, gridExtra, ggplot2, methods, stats, grid, MASS, calibrate, gplots, edgeR, limma, foreach, affy Suggests: RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>= 1.3), roxygen2, doSNOW License: GPL-2 Package: Statial Version: 1.6.0 Depends: R (>= 4.1.0) Imports: BiocParallel, spatstat.geom, concaveman, data.table, spatstat.explore, dplyr, tidyr, SingleCellExperiment, tibble, stringr, tidyselect, ggplot2, methods, stats, SummarizedExperiment, S4Vectors, plotly, purrr, ranger, magrittr, limma, SpatialExperiment Suggests: BiocStyle, knitr, testthat (>= 3.0.0), ClassifyR, spicyR, ggsurvfit, lisaClust, survival License: GPL-3 Package: statTarget Version: 1.34.0 Depends: R (>= 3.6.0) Imports: randomForest,plyr,pdist,ROC,utils,grDevices,graphics,rrcov,stats, pls,impute Suggests: testthat, BiocStyle, knitr, rmarkdown License: LGPL (>= 3) Package: STdeconvolve Version: 1.8.0 Depends: R (>= 4.1) Imports: topicmodels, BiocParallel, Matrix, methods, mgcv, ggplot2, scatterpie, viridis, slam, stats, clue, liger, reshape2, graphics, grDevices, utils Suggests: knitr, BiocStyle, rmarkdown, testthat, rcmdcheck, gplots, gridExtra, hash, dplyr, parallel License: GPL-3 Package: stepNorm Version: 1.76.0 Depends: R (>= 1.8.0), marray, methods Imports: marray, MASS, methods, stats License: LGPL Package: stJoincount Version: 1.6.0 Depends: R (>= 4.2.0) Imports: graphics, stats, dplyr, magrittr, sp, raster, spdep, ggplot2, pheatmap, grDevices, Seurat, SpatialExperiment, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE Package: strandCheckR Version: 1.22.0 Imports: dplyr, magrittr, GenomeInfoDb, GenomicAlignments, GenomicRanges, IRanges, Rsamtools, S4Vectors, grid, BiocGenerics, ggplot2, reshape2, stats, gridExtra, TxDb.Hsapiens.UCSC.hg38.knownGene, methods, stringr, rmarkdown Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) Package: Streamer Version: 1.50.0 Imports: methods, graph, RBGL, parallel, BiocGenerics Suggests: RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz License: Artistic-2.0 Archs: x64 Package: STRINGdb Version: 2.16.4 Depends: R (>= 2.14.0) Imports: png, sqldf, plyr, igraph, httr, methods, RColorBrewer, gplots, hash, plotrix Suggests: RUnit, BiocGenerics License: GPL-2 Package: STROMA4 Version: 1.28.0 Depends: R (>= 3.4), Biobase, BiocParallel, cluster, matrixStats, stats, graphics, utils Suggests: breastCancerMAINZ License: GPL-3 Package: struct Version: 1.16.0 Depends: R (>= 4.0) Imports: methods,ontologyIndex, datasets, graphics, stats, utils, knitr, SummarizedExperiment, S4Vectors, rols Suggests: testthat, rstudioapi, rmarkdown, covr, BiocStyle, openxlsx, ggplot2, magick License: GPL-3 Package: Structstrings Version: 1.20.0 Depends: R (>= 4.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), Biostrings (>= 2.57.2) Imports: methods, BiocGenerics, XVector, stringr, stringi, crayon, grDevices LinkingTo: IRanges, S4Vectors Suggests: testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle License: Artistic-2.0 Archs: x64 Package: structToolbox Version: 1.16.0 Depends: R (>= 4.0), struct (>= 1.5.1) Imports: ggplot2, ggthemes, grid, gridExtra, methods, scales, sp, stats Suggests: agricolae, BiocFileCache, BiocStyle, car, covr, cowplot, e1071, emmeans, ggdendro, knitr, magick, nlme, openxlsx, pls, pmp, reshape2, ropls, rmarkdown, Rtsne, testthat, rappdirs License: GPL-3 Package: StructuralVariantAnnotation Version: 1.20.0 Depends: GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R (>= 4.1.0) Imports: assertthat, Biostrings, pwalign, stringr, dplyr, methods, rlang, GenomicFeatures, IRanges, S4Vectors, SummarizedExperiment, GenomeInfoDb, Suggests: ggplot2, devtools, testthat (>= 2.1.0), roxygen2, rmarkdown, tidyverse, knitr, ggbio, biovizBase, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, License: GPL-3 + file LICENSE Package: SubCellBarCode Version: 1.20.0 Depends: R (>= 3.6) Imports: Rtsne, scatterplot3d, caret, e1071, ggplot2, gridExtra, networkD3, ggrepel, graphics, stats, org.Hs.eg.db, AnnotationDbi Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 Package: subSeq Version: 1.34.0 Depends: R (>= 3.2) Imports: data.table, dplyr, tidyr, ggplot2, magrittr, qvalue (>= 1.99), digest, Biobase Suggests: limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr License: MIT + file LICENSE Package: SUITOR Version: 1.6.0 Depends: R (>= 4.2.0) Imports: stats, utils, graphics, ggplot2, BiocParallel Suggests: devtools, MutationalPatterns, RUnit, BiocManager, BiocGenerics, BiocStyle, knitr, rmarkdown License: GPL-2 Archs: x64 Package: SummarizedExperiment Version: 1.34.0 Depends: R (>= 4.0.0), methods, MatrixGenerics (>= 1.1.3), GenomicRanges (>= 1.55.2), Biobase Imports: utils, stats, tools, Matrix, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.33.7), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.13.1), S4Arrays (>= 1.1.1), DelayedArray (>= 0.27.1) Suggests: HDF5Array (>= 1.7.5), annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, jsonlite, rhdf5, airway (>= 1.15.1), BiocStyle, knitr, rmarkdown, RUnit, testthat, digest License: Artistic-2.0 Package: Summix Version: 2.10.0 Depends: R (>= 4.3) Imports: dplyr, nloptr, magrittr, methods, tibble, tidyselect, BEDASSLE, scales, visNetwork, randomcoloR Suggests: rmarkdown, markdown, knitr, testthat (>= 3.0.0) License: MIT + file LICENSE Package: supersigs Version: 1.12.0 Depends: R (>= 4.1) Imports: assertthat, caret, dplyr, tidyr, rsample, methods, rlang, utils, Biostrings, stats, SummarizedExperiment Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, testthat, VariantAnnotation License: GPL-3 Package: supraHex Version: 1.42.0 Depends: R (>= 3.6), hexbin Imports: ape, MASS, grDevices, graphics, stats, readr, tibble, tidyr, dplyr, stringr, purrr, magrittr, igraph, methods License: GPL-2 Package: surfaltr Version: 1.10.0 Depends: R (>= 4.0) Imports: dplyr (>= 1.0.6), biomaRt (>= 2.46.0), protr (>= 1.6-2), seqinr (>= 4.2-5), ggplot2 (>= 3.3.2), utils (>= 2.10.1), stringr (>= 1.4.0), Biostrings (>= 2.58.0),readr (>= 1.4.0), httr (>= 1.4.2), testthat(>= 3.0.0), xml2(>= 1.3.2), msa (>= 1.22.0), methods (>= 4.0.3) Suggests: knitr, rmarkdown, devtools, kableExtra License: MIT + file LICENSE Package: SurfR Version: 1.0.0 Depends: R (>= 4.3.0) Imports: httr, BiocFileCache, BiocStyle, SPsimSeq, DESeq2, edgeR, openxlsx, stringr, rhdf5, ggplot2, ggrepel, stats, magrittr, assertr, tidyr, dplyr, TCGAbiolinks, biomaRt, metaRNASeq, enrichR, scales, venn, gridExtra, SummarizedExperiment, knitr, grDevices, graphics, utils Suggests: testthat (>= 3.0.0) License: GPL-3 + file LICENSE Package: survcomp Version: 1.54.0 Depends: survival, prodlim, R (>= 3.4) Imports: ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid, rmeta, stats, graphics Suggests: Hmisc, clinfun, xtable, Biobase, BiocManager License: Artistic-2.0 Archs: x64 Package: survtype Version: 1.20.0 Depends: SummarizedExperiment, pheatmap, survival, survminer, clustvarsel, stats, utils Suggests: maftools, scales, knitr, rmarkdown License: Artistic-2.0 Package: sva Version: 3.52.0 Depends: R (>= 3.2), mgcv, genefilter, BiocParallel Imports: matrixStats, stats, graphics, utils, limma, edgeR Suggests: pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat License: Artistic-2.0 Archs: x64 Package: svaNUMT Version: 1.10.0 Depends: GenomicRanges, rtracklayer, VariantAnnotation, StructuralVariantAnnotation, BiocGenerics, Biostrings, R (>= 4.0) Imports: assertthat, stringr, dplyr, methods, rlang, GenomeInfoDb, S4Vectors, GenomicFeatures, pwalign Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, readr, plyranges, circlize, IRanges, SummarizedExperiment, rmarkdown License: GPL-3 + file LICENSE Package: svaRetro Version: 1.10.0 Depends: GenomicRanges, rtracklayer, BiocGenerics, StructuralVariantAnnotation, R (>= 4.0) Imports: VariantAnnotation, assertthat, Biostrings, stringr, dplyr, methods, rlang, GenomicFeatures, GenomeInfoDb, S4Vectors, utils Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, BiocStyle, plyranges, circlize, tictoc, IRanges, stats, SummarizedExperiment, rmarkdown License: GPL-3 + file LICENSE Package: SVMDO Version: 1.4.0 Depends: R(>= 4.3), shiny (>= 1.7.4) Imports: shinyFiles (>= 0.9.3), shinytitle (>= 0.1.0), golem (>= 0.3.5), nortest (>= 1.0-4), e1071 (>= 1.7-12), BSDA (>= 1.2.1), data.table (>= 1.14.6), sjmisc (>= 2.8.9), klaR (>= 1.7-1), caTools (>= 1.18.2), caret (>= 6.0-93), survival (>= 3.4-0), DOSE (>= 3.24.2), AnnotationDbi (>= 1.60.0), org.Hs.eg.db (>= 3.16.0), dplyr (>= 1.0.10), SummarizedExperiment (>= 1.28.0), grDevices, graphics, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.1.6) License: GPL-3 Package: SWATH2stats Version: 1.34.0 Depends: R(>= 2.10.0) Imports: data.table, reshape2, ggplot2, stats, grDevices, graphics, utils, biomaRt, methods Suggests: testthat, knitr, rmarkdown Enhances: MSstats, PECA, aLFQ License: GPL-3 Package: SwathXtend Version: 2.26.0 Depends: e1071, openxlsx, VennDiagram, lattice License: GPL-2 Package: swfdr Version: 1.30.0 Depends: R (>= 3.4) Imports: methods, splines, stats4, stats Suggests: dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2, rmarkdown, testthat License: GPL (>= 3) Package: switchBox Version: 1.40.0 Depends: R (>= 2.13.1), pROC, gplots License: GPL-2 Archs: x64 Package: switchde Version: 1.30.0 Depends: R (>= 3.4), SingleCellExperiment Imports: SummarizedExperiment, dplyr, ggplot2, methods, stats Suggests: knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr License: GPL (>= 2) Package: synapsis Version: 1.10.0 Depends: R (>= 4.1) Imports: EBImage, stats, utils, graphics Suggests: knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, tidyverse, BiocStyle License: MIT + file LICENSE Package: synapter Version: 2.28.0 Depends: R (>= 3.1.0), methods, MSnbase (>= 2.1.2) Imports: RColorBrewer, lattice, qvalue, multtest, utils, tools, Biobase, Biostrings, cleaver (>= 1.3.3), readr (>= 0.2), rmarkdown (>= 1.0) Suggests: synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN, BiocStyle, knitr License: GPL-2 Package: synergyfinder Version: 3.12.0 Depends: R (>= 4.0.0) Imports: drc (>= 3.0-1), reshape2 (>= 1.4.4), tidyverse (>= 1.3.0), dplyr (>= 1.0.3), tidyr (>= 1.1.2), purrr (>= 0.3.4), furrr (>= 0.2.2), ggplot2 (>= 3.3.3), ggforce (>= 0.3.2), grid (>= 4.0.2), vegan (>= 2.5-7), gstat (>= 2.0-6), sp (>= 1.4-5), methods (>= 4.0.2), SpatialExtremes (>= 2.0-9), ggrepel (>= 0.9.1), kriging (>= 1.1), plotly (>= 4.9.3), stringr (>= 1.4.0), future (>= 1.21.0), mice (>= 3.13.0), lattice (>= 0.20-41), nleqslv (>= 3.3.2), stats (>= 4.0.2), graphics (>= 4.0.2), grDevices (>= 4.0.2), magrittr (>= 2.0.1), pbapply (>= 1.4-3), metR (>= 0.9.1) Suggests: knitr, rmarkdown License: Mozilla Public License 2.0 Package: SynExtend Version: 1.16.0 Depends: R (>= 4.3.0), DECIPHER (>= 2.28.0) Imports: methods, Biostrings, S4Vectors, IRanges, utils, stats, parallel, graphics, grDevices, RSQLite, DBI Suggests: BiocStyle, knitr, igraph, markdown, rmarkdown License: GPL-3 Archs: x64 Package: synlet Version: 2.4.0 Depends: R (>= 3.5.0) Imports: data.table, ggplot2, grDevices, magrittr, methods, patchwork, RankProd, RColorBrewer, stats, utils Suggests: BiocStyle, knitr, testthat, rmarkdown License: GPL-3 Package: SynMut Version: 1.20.0 Imports: seqinr, methods, Biostrings, stringr, BiocGenerics Suggests: BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc, glue License: GPL-2 Package: syntenet Version: 1.6.0 Depends: R (>= 4.2) Imports: Rcpp (>= 1.0.8), BiocParallel, GenomicRanges, rlang, Biostrings, rtracklayer, utils, methods, igraph, stats, grDevices, RColorBrewer, pheatmap, ggplot2, ggnetwork, intergraph, networkD3 LinkingTo: Rcpp, testthat Suggests: BiocStyle, ggtree, labdsv, covr, knitr, rmarkdown, testthat (>= 3.0.0), xml2 License: GPL-3 Archs: x64 Package: systemPipeR Version: 2.10.0 Depends: Rsamtools (>= 1.31.2), Biostrings, ShortRead (>= 1.37.1), methods Imports: GenomicRanges, SummarizedExperiment, ggplot2, yaml, stringr, magrittr, S4Vectors, crayon, BiocGenerics, htmlwidgets Suggests: BiocStyle, knitr, rmarkdown, systemPipeRdata, GenomicAlignments, grid, dplyr, testthat, rjson, annotate, AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT, rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools, GenomicFeatures, txdbmaker, VariantAnnotation (>= 1.25.11) License: Artistic-2.0 Package: systemPipeShiny Version: 1.14.0 Depends: R (>= 4.0.0), shiny (>= 1.6.0), spsUtil (>= 0.2.2), spsComps (>= 0.3.3), drawer (>= 0.2) Imports: DT, assertthat, bsplus, crayon, dplyr, ggplot2, htmltools, glue, magrittr, methods, plotly, rlang, rstudioapi, shinyAce, shinyFiles, shinyWidgets, shinydashboard, shinydashboardPlus (>= 2.0.0), shinyjqui, shinyjs, shinytoastr, stringr, stats, styler, tibble, utils, vroom (>= 1.3.1), yaml, R6, RSQLite, openssl Suggests: testthat, BiocStyle, knitr, rmarkdown, systemPipeR (>= 2.2.0), systemPipeRdata (>= 2.0.0), rhandsontable, zip, callr, pushbar, fs, readr, R.utils, DESeq2, SummarizedExperiment, glmpca, pheatmap, grid, ape, Rtsne, UpSetR, tidyr, esquisse (>= 1.1.0), cicerone License: GPL (>= 3) Package: systemPipeTools Version: 1.12.0 Imports: DESeq2, GGally, Rtsne, SummarizedExperiment, ape, dplyr, ggplot2, ggrepel, ggtree, glmpca, pheatmap, plotly, tibble, magrittr, DT, stats Suggests: systemPipeR, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocGenerics, Biostrings, methods License: Artistic-2.0 Package: tadar Version: 1.2.1 Depends: GenomicRanges, ggplot2, R (>= 4.3.0) Imports: BiocGenerics, GenomeInfoDb, Gviz, IRanges, MatrixGenerics, methods, rlang, Rsamtools, S4Vectors, stats, VariantAnnotation Suggests: BiocStyle, covr, knitr, limma, rmarkdown, testthat (>= 3.0.0), tidyverse License: GPL-3 Package: TADCompare Version: 1.14.0 Depends: R (>= 4.0) Imports: dplyr, PRIMME, cluster, Matrix, magrittr, HiCcompare, ggplot2, tidyr, ggpubr, RColorBrewer, reshape2, cowplot Suggests: BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr, pheatmap, SpectralTAD, magick, qpdf License: MIT + file LICENSE Package: tanggle Version: 1.10.0 Depends: R (>= 4.1), ggplot2 (>= 2.2.0), ggtree Imports: ape (>= 5.0), phangorn (>= 2.5), utils, methods Suggests: tinytest, BiocStyle, ggimage, knitr, rmarkdown License: Artistic-2.0 Package: TAPseq Version: 1.16.0 Depends: R (>= 4.0.0) Imports: methods, GenomicAlignments, GenomicRanges, IRanges, BiocGenerics, S4Vectors (>= 0.20.1), GenomeInfoDb, BSgenome, GenomicFeatures, Biostrings, dplyr, tidyr, BiocParallel Suggests: testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer, BiocStyle License: MIT + file LICENSE Package: target Version: 1.18.0 Depends: R (>= 3.6) Imports: BiocGenerics, GenomicRanges, IRanges, matrixStats, methods, stats, graphics, shiny Suggests: testthat (>= 2.1.0), knitr, rmarkdown, shinytest, shinyBS, covr License: GPL-3 Package: TargetDecoy Version: 1.10.0 Depends: R (>= 4.1) Imports: ggplot2, ggpubr, methods, miniUI, mzID, mzR, shiny, stats Suggests: BiocStyle, knitr, msdata, sessioninfo, rmarkdown, gridExtra, testthat (>= 3.0.0), covr License: Artistic-2.0 Package: TargetScore Version: 1.42.0 Depends: pracma, Matrix Suggests: TargetScoreData, gplots, Biobase, GEOquery License: GPL-2 Package: TargetSearch Version: 2.6.2 Imports: graphics, grDevices, methods, ncdf4, stats, utils, assertthat Suggests: TargetSearchData, BiocStyle, knitr, tinytest License: GPL (>= 2) Archs: x64 Package: TBSignatureProfiler Version: 1.16.0 Depends: R (>= 4.2.0) Imports: ASSIGN (>= 1.23.1), BiocParallel, ComplexHeatmap, DESeq2, DT, edgeR, gdata, ggplot2, GSVA (>= 1.51.3), magrittr, methods, RColorBrewer, reshape2, rlang, ROCit, S4Vectors, singscore, stats, SummarizedExperiment Suggests: BiocStyle, caret, circlize, class, covr, dplyr, e1071, glmnet, HGNChelper, impute, knitr, lintr, MASS, plyr, pROC, randomForest, rmarkdown, shiny, spelling, sva, testthat License: MIT + file LICENSE Package: TCC Version: 1.44.0 Depends: R (>= 3.0), methods, DESeq2, edgeR, ROC Suggests: RUnit, BiocGenerics License: GPL-2 Package: TCGAbiolinks Version: 2.32.0 Depends: R (>= 4.0) Imports: downloader (>= 0.4), grDevices, biomaRt, dplyr, graphics, tibble, GenomicRanges, XML (>= 3.98.0), data.table, jsonlite (>= 1.0.0), plyr, knitr, methods, ggplot2, stringr (>= 1.0.0), IRanges, rvest (>= 0.3.0), stats, utils, S4Vectors, R.utils, SummarizedExperiment (>= 1.4.0), TCGAbiolinksGUI.data (>= 1.15.1), readr, tools, tidyr, purrr, xml2, httr (>= 1.2.1) Suggests: jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, Biobase, affy, testthat, sesame, AnnotationHub, ExperimentHub, pathview, clusterProfiler, Seurat, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph, supraHex, limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3), scales, grid, DT License: GPL (>= 3) Package: TCGAutils Version: 1.24.0 Depends: R (>= 4.2.0) Imports: AnnotationDbi, BiocGenerics, BiocBaseUtils, GenomeInfoDb, GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges, methods, MultiAssayExperiment, RaggedExperiment (>= 1.5.7), rvest, S4Vectors, stats, stringr, SummarizedExperiment, utils, xml2 Suggests: AnnotationHub, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, httr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, RColorBrewer, readr, rmarkdown, RTCGAToolbox (>= 2.17.4), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 Package: TCseq Version: 1.28.0 Depends: R (>= 3.4) Imports: edgeR, BiocGenerics, reshape2, GenomicRanges, IRanges, SummarizedExperiment, GenomicAlignments, Rsamtools, e1071, cluster, ggplot2, grid, grDevices, stats, utils, methods, locfit Suggests: testthat License: GPL (>= 2) Package: TDbasedUFE Version: 1.4.0 Imports: GenomicRanges, rTensor, readr, methods, MOFAdata, tximport, tximportData, graphics, stats, utils, shiny Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 Package: TDbasedUFEadv Version: 1.4.0 Imports: TDbasedUFE, Biobase, GenomicRanges, utils, rTensor, methods, graphics, RTCGA, stats, enrichplot, DOSE, STRINGdb, enrichR, hash, shiny Suggests: knitr, rmarkdown, testthat (>= 3.0.0), RTCGA.rnaseq, RTCGA.clinical, BiocStyle, MOFAdata License: GPL-3 Package: TEKRABber Version: 1.8.0 Depends: R (>= 4.3) Imports: apeglm, biomaRt, dplyr, doParallel, DESeq2, foreach, GenomeInfoDb, magrittr, Rcpp (>= 1.0.7), rtracklayer, SCBN, stats, utils LinkingTo: Rcpp Suggests: BiocStyle, bslib, ggplot2, ggpubr, plotly, rmarkdown, shiny, knitr, testthat (>= 3.0.0) License: LGPL (>= 3) Archs: x64 Package: TENxIO Version: 1.6.0 Depends: R (>= 4.2.0), SingleCellExperiment, SummarizedExperiment Imports: BiocBaseUtils, BiocGenerics, BiocIO, GenomeInfoDb, GenomicRanges, Matrix, MatrixGenerics, methods, RCurl, readr, R.utils, S4Vectors, utils Suggests: BiocStyle, DropletTestFiles, ExperimentHub, HDF5Array, knitr, RaggedExperiment, rhdf5, rmarkdown, Rsamtools, tinytest License: Artistic-2.0 Package: TEQC Version: 4.26.0 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Rsamtools, hwriter Imports: Biobase (>= 2.15.1) License: GPL (>= 2) Package: ternarynet Version: 1.48.0 Depends: R (>= 4.0) Imports: utils, igraph, methods, graphics, stats, BiocParallel Suggests: testthat Enhances: Rmpi, snow License: GPL (>= 2) Archs: x64 Package: terraTCGAdata Version: 1.8.0 Depends: R (>= 4.2.0), AnVIL, MultiAssayExperiment Imports: BiocFileCache, dplyr, GenomicRanges, methods, RaggedExperiment, readr, S4Vectors, stats, tidyr, TCGAutils, utils Suggests: knitr, rmarkdown, BiocStyle, withr, testthat (>= 3.0.0) License: Artistic-2.0 Package: TFARM Version: 1.26.0 Depends: R (>= 3.5.0) Imports: arules, fields, GenomicRanges, graphics, stringr, methods, stats, gplots Suggests: BiocStyle, knitr, plyr License: Artistic-2.0 Package: TFBSTools Version: 1.42.0 Depends: R (>= 3.2.2) Imports: Biobase(>= 2.28), Biostrings(>= 2.36.4), pwalign, BiocGenerics(>= 0.14.0), BiocParallel(>= 1.2.21), BSgenome(>= 1.36.3), caTools(>= 1.17.1), CNEr(>= 1.4.0), DirichletMultinomial(>= 1.10.0), GenomeInfoDb(>= 1.6.1), GenomicRanges(>= 1.20.6), gtools(>= 3.5.0), grid, IRanges(>= 2.2.7), methods, DBI (>= 0.6), RSQLite(>= 1.0.0), rtracklayer(>= 1.28.10), seqLogo(>= 1.34.0), S4Vectors(>= 0.9.25), TFMPvalue(>= 0.0.5), XML(>= 3.98-1.3), XVector(>= 0.8.0), parallel Suggests: BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr(>= 1.11), testthat, JASPAR2016(>= 1.0.0), JASPAR2018(>= 1.0.0), rmarkdown License: GPL-2 Archs: x64 Package: TFEA.ChIP Version: 1.24.0 Depends: R (>= 3.5) Imports: GenomicRanges, IRanges, biomaRt, GenomicFeatures, grDevices, dplyr, stats, utils, R.utils, methods, org.Hs.eg.db Suggests: knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2, DESeq2, BiocGenerics, ggrepel, rcompanion, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit License: Artistic-2.0 Package: TFHAZ Version: 1.26.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, S4Vectors, grDevices, graphics, stats, utils, IRanges, methods, ORFik Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 Package: TFutils Version: 1.24.0 Depends: R (>= 4.1.0) Imports: methods, dplyr, magrittr, miniUI, shiny, Rsamtools, GSEABase, rjson, BiocFileCache, DT, httr, readxl, AnnotationDbi, org.Hs.eg.db, utils Suggests: knitr, data.table, testthat, AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges, S4Vectors, EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, GenomicFiles, GenomeInfoDb, SummarizedExperiment, UpSetR, ggplot2, png, gwascat, MotifDb, motifStack, RColorBrewer, rmarkdown License: Artistic-2.0 Package: tidybulk Version: 1.16.0 Depends: R (>= 4.1.0), ttservice (>= 0.3.6) Imports: tibble, readr, dplyr (>= 1.1.0), magrittr, tidyr, stringi, stringr, rlang, purrr, tidyselect, preprocessCore, stats, parallel, utils, lifecycle, scales, SummarizedExperiment, GenomicRanges, methods, S4Vectors, crayon, Matrix Suggests: BiocStyle, testthat, vctrs, AnnotationDbi, BiocManager, Rsubread, e1071, edgeR, limma, org.Hs.eg.db, org.Mm.eg.db, sva, GGally, knitr, qpdf, covr, Seurat, KernSmooth, Rtsne, ggplot2, widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel, devtools, functional, survminer, tidySummarizedExperiment, markdown, uwot, matrixStats, igraph, EGSEA, IRanges, here, glmmSeq, pbapply, pbmcapply, lme4, glmmTMB, MASS, pkgconfig License: GPL-3 Package: tidyCoverage Version: 1.0.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, BiocParallel, BiocIO, rtracklayer, methods, tidyr, dplyr, fansi, pillar, rlang, cli, purrr, vctrs, stats Suggests: tidySummarizedExperiment, plyranges, ggplot2, TxDb.Hsapiens.UCSC.hg19.knownGene, AnnotationHub, GenomicFeatures, BiocStyle, hues, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE Package: tidyomics Version: 1.0.0 Depends: R (>= 4.2) Imports: tidySummarizedExperiment, tidySingleCellExperiment, tidyseurat, tidybulk, plyranges, nullranges, purrr, rlang, stringr, cli, utils Suggests: tidyr, dplyr, tibble, ggplot2, mockr (>= 0.2.0), knitr (>= 1.41), rmarkdown (>= 2.20), testthat (>= 3.1.6) License: MIT + file LICENSE Package: tidySingleCellExperiment Version: 1.14.0 Depends: R (>= 4.3.0), SingleCellExperiment Imports: dplyr, tidyr, ttservice (>= 0.4.0), SummarizedExperiment, tibble, ggplot2, magrittr, rlang, purrr, pkgconfig, lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi, Matrix, stats Suggests: BiocStyle, testthat, knitr, rmarkdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, uwot, celldex, dittoSeq, plotly License: GPL-3 Package: tidySpatialExperiment Version: 1.0.0 Depends: R (>= 4.3.0), SpatialExperiment, tidySingleCellExperiment Imports: ttservice, SummarizedExperiment, SingleCellExperiment, BiocGenerics, Matrix, S4Vectors, methods, utils, pkgconfig, tibble, dplyr, tidyr, ggplot2, magrittr, rlang, purrr, stringr, vctrs, tidyselect, pillar, cli, fansi, lifecycle Suggests: BiocStyle, testthat, knitr, markdown, SingleCellSignalR, SingleR, scater, scran, igraph, GGally, celldex, dittoSeq, cowplot, DropletUtils, plotly, tidySummarizedExperiment License: GPL-3 Package: tidySummarizedExperiment Version: 1.14.0 Depends: R (>= 4.3.0), SummarizedExperiment, ttservice (>= 0.4.0) Imports: dplyr, tibble (>= 3.0.4), magrittr, tidyr, ggplot2, rlang, purrr, lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi, stats, pkgconfig Suggests: BiocStyle, testthat, knitr, markdown, plotly License: GPL-3 Package: tigre Version: 1.58.0 Depends: R (>= 2.11.0), BiocGenerics, Biobase Imports: methods, AnnotationDbi, gplots, graphics, grDevices, stats, utils, annotate, DBI, RSQLite Suggests: drosgenome1.db, puma, lumi, BiocStyle, BiocManager License: AGPL-3 Archs: x64 Package: TileDBArray Version: 1.14.0 Depends: DelayedArray (>= 0.27.2) Imports: methods, Rcpp, tiledb, S4Vectors LinkingTo: Rcpp Suggests: knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat License: MIT + file LICENSE Archs: x64 Package: tilingArray Version: 1.82.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 License: Artistic-2.0 Archs: x64 Package: timecourse Version: 1.76.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL Package: timeOmics Version: 1.16.0 Depends: mixOmics, R (>= 4.0) Imports: dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr, ggrepel, lmtest, plyr, checkmate Suggests: BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse, igraph, gplots License: GPL-3 Package: timescape Version: 1.28.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), stringr (>= 1.0.0), dplyr (>= 0.4.3), gtools (>= 3.5.0) Suggests: knitr, rmarkdown License: GPL-3 Package: TIN Version: 1.36.0 Depends: R (>= 2.12.0), data.table, impute, aroma.affymetrix Imports: WGCNA, squash, stringr Suggests: knitr, aroma.light, affxparser, RUnit, BiocGenerics License: Artistic-2.0 Package: TissueEnrich Version: 1.24.1 Depends: R (>= 3.5), ggplot2 (>= 2.2.1), SummarizedExperiment (>= 1.6.5), GSEABase (>= 1.38.2) Imports: dplyr (>= 0.7.3), tidyr (>= 0.8.0), stats Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE Package: TitanCNA Version: 1.42.0 Depends: R (>= 3.5.1) Imports: BiocGenerics (>= 0.31.6), IRanges (>= 2.6.1), GenomicRanges (>= 1.24.3), VariantAnnotation (>= 1.18.7), foreach (>= 1.4.3), GenomeInfoDb (>= 1.8.7), data.table (>= 1.10.4), dplyr (>= 0.5.0), License: GPL-3 Archs: x64 Package: tkWidgets Version: 1.82.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0), tools Suggests: Biobase, hgu95av2 License: Artistic-2.0 Package: tLOH Version: 1.12.0 Depends: R (>= 4.2) Imports: scales, stats, utils, ggplot2, data.table, purrr, dplyr, VariantAnnotation, GenomicRanges, MatrixGenerics, bestNormalize, depmixS4, naniar, stringr Suggests: knitr, rmarkdown License: MIT + file LICENSE Package: TMixClust Version: 1.26.0 Depends: R (>= 3.4) Imports: gss, mvtnorm, stats, zoo, cluster, utils, BiocParallel, flexclust, grDevices, graphics, Biobase, SPEM Suggests: rmarkdown, knitr, BiocStyle, testthat License: GPL (>= 2) Package: TOAST Version: 1.18.0 Depends: R (>= 3.6), EpiDISH, limma, nnls, quadprog Imports: stats, methods, SummarizedExperiment, corpcor, doParallel, parallel, ggplot2, tidyr, GGally Suggests: BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix License: GPL-2 Package: tomoda Version: 1.14.0 Depends: R (>= 4.0.0) Imports: methods, stats, grDevices, reshape2, Rtsne, umap, RColorBrewer, ggplot2, ggrepel, SummarizedExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat License: MIT + file LICENSE Package: tomoseqr Version: 1.8.0 Depends: R (>= 4.2) Imports: grDevices, graphics, animation, tibble, dplyr, stringr, purrr, methods, shiny, BiocFileCache, readr, tools, plotly, ggplot2 Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE Package: TOP Version: 1.4.0 Depends: R (>= 3.5.0) Imports: assertthat, caret, ClassifyR, directPA, doParallel, dplyr, ggnewscale, ggplot2, ggraph, ggrepel, ggthemes, glmnet, Hmisc, igraph, latex2exp, limma, magrittr, methods, plotly, pROC, purrr, reshape2, stats, stringr, survival, tibble, tidygraph, tidyr, statmod Suggests: knitr, rmarkdown, BiocStyle, Biobase, curatedOvarianData, ggbeeswarm, ggsci, survminer, tidyverse License: GPL-3 Package: topconfects Version: 1.20.0 Depends: R (>= 3.6.0) Imports: methods, utils, stats, assertthat, ggplot2 Suggests: limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr, rmarkdown, BiocStyle License: LGPL-2.1 | file LICENSE Package: topdownr Version: 1.26.0 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.20.0), ProtGenerics (>= 1.10.0), Biostrings (>= 2.42.1), S4Vectors (>= 0.12.2) Imports: grDevices, stats, tools, utils, Biobase, Matrix (>= 1.4-2), MSnbase (>= 2.3.10), PSMatch (>= 1.6.0), ggplot2 (>= 2.2.1), mzR (>= 2.27.5) Suggests: topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat, BiocStyle, xml2 License: GPL (>= 3) Package: topGO Version: 2.56.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.6), graph (>= 1.14.0), Biobase (>= 2.0.0), GO.db (>= 2.3.0), AnnotationDbi (>= 1.7.19), SparseM (>= 0.73) Imports: lattice, matrixStats, DBI Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest License: LGPL Package: ToxicoGx Version: 2.8.0 Depends: R (>= 4.1), CoreGx Imports: SummarizedExperiment, BiocGenerics, S4Vectors, Biobase, BiocParallel, ggplot2, tibble, dplyr, caTools, downloader, magrittr, methods, reshape2, tidyr, data.table, assertthat, scales, graphics, grDevices, parallel, stats, utils, limma, jsonlite Suggests: rmarkdown, testthat, BiocStyle, knitr, tinytex, devtools, PharmacoGx, xtable, markdown License: MIT + file LICENSE Package: TPP2D Version: 1.20.0 Depends: R (>= 3.6.0), stats, utils, dplyr, methods Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl, parallel, MASS, BiocParallel, limma Suggests: knitr, testthat, rmarkdown, BiocStyle License: GPL-3 Package: TPP Version: 3.32.0 Depends: R (>= 3.4), Biobase, dplyr, magrittr, tidyr Imports: biobroom, broom, data.table, doParallel, foreach, futile.logger, ggplot2, grDevices, gridExtra, grid, knitr, limma, MASS, mefa, nls2, openxlsx (>= 2.4.0), parallel, plyr, purrr, RColorBrewer, RCurl, reshape2, rmarkdown, splines, stats, stringr, tibble, utils, VennDiagram, VGAM Suggests: BiocStyle, testthat License: Artistic-2.0 Package: tpSVG Version: 1.0.0 Depends: mgcv, R (>= 4.4) Imports: stats, BiocParallel, MatrixGenerics, methods, SingleCellExperiment, SummarizedExperiment, SpatialExperiment Suggests: BiocStyle, knitr, nnSVG, rmarkdown, scran, scuttle, STexampleData, escheR, ggpubr, colorspace, BumpyMatrix, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE Package: tracktables Version: 1.38.0 Depends: R (>= 3.5.0) Imports: IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base, stringr, RColorBrewer, methods Suggests: knitr, BiocStyle License: GPL (>= 3) Package: trackViewer Version: 1.40.0 Depends: R (>= 3.5.0), grDevices, methods, GenomicRanges, grid Imports: GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz, Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools, IRanges, AnnotationDbi, grImport, htmlwidgets, plotrix, InteractionSet, igraph, utils, rhdf5, strawr, txdbmaker Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown, motifStack License: GPL (>= 2) Package: tradeSeq Version: 1.18.0 Depends: R (>= 3.6) Imports: mgcv, edgeR, SingleCellExperiment, SummarizedExperiment, slingshot, magrittr, RColorBrewer, BiocParallel, Biobase, pbapply, igraph, ggplot2, princurve, methods, S4Vectors, tibble, Matrix, TrajectoryUtils, viridis, matrixStats, MASS Suggests: knitr, rmarkdown, testthat, covr, clusterExperiment, DelayedMatrixStats License: MIT + file LICENSE Package: TrajectoryGeometry Version: 1.12.0 Depends: R (>= 4.1) Imports: pracma, rgl, ggplot2, stats, methods Suggests: dplyr, knitr, RColorBrewer, rmarkdown License: MIT + file LICENSE Package: TrajectoryUtils Version: 1.12.0 Depends: SingleCellExperiment Imports: methods, stats, Matrix, igraph, S4Vectors, SummarizedExperiment Suggests: BiocNeighbors, DelayedArray, DelayedMatrixStats, BiocParallel, testthat, knitr, BiocStyle, rmarkdown License: GPL-3 Package: transcriptogramer Version: 1.26.0 Depends: R (>= 3.4), methods Imports: biomaRt, data.table, doSNOW, foreach, ggplot2, graphics, grDevices, igraph, limma, parallel, progress, RedeR, snow, stats, tidyr, topGO Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: GPL (>= 2) Package: transcriptR Version: 1.32.0 Depends: R (>= 3.5.0), methods Imports: BiocGenerics, caret, chipseq, e1071, GenomicAlignments, GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2, graphics, grDevices, IRanges (>= 2.11.15), pROC, reshape2, Rsamtools, rtracklayer, S4Vectors, stats, utils Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat License: GPL-3 Package: transformGamPoi Version: 1.10.0 Imports: glmGamPoi, DelayedArray, Matrix, MatrixGenerics, SummarizedExperiment, HDF5Array, methods, utils, Rcpp LinkingTo: Rcpp Suggests: testthat, TENxPBMCData, scran, knitr, rmarkdown, BiocStyle License: GPL-3 Archs: x64 Package: transite Version: 1.22.0 Depends: R (>= 3.5) Imports: BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>= 0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0), grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>= 1.0.4.8), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), utils LinkingTo: Rcpp (>= 1.0.4.8) Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE Archs: x64 Package: tRanslatome Version: 1.42.0 Depends: R (>= 2.15.0), methods, limma, anota, DESeq2, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix, Biobase License: GPL-3 Package: transmogR Version: 1.0.0 Depends: Biostrings, GenomicRanges Imports: BSgenome, GenomeInfoDb, GenomicFeatures, ggplot2 (>= 3.5.0), IRanges, methods, parallel, rlang, scales, stats, S4Vectors, SummarizedExperiment, VariantAnnotation Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, ComplexUpset, extraChIPs, InteractionSet, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0) License: GPL-3 Package: transomics2cytoscape Version: 1.14.0 Imports: RCy3, KEGGREST, dplyr, purrr, tibble, pbapply Suggests: testthat, roxygen2, knitr, BiocStyle, rmarkdown License: Artistic-2.0 Package: TransView Version: 1.48.0 Depends: methods, GenomicRanges Imports: BiocGenerics, S4Vectors (>= 0.9.25), IRanges, zlibbioc, gplots LinkingTo: Rhtslib (>= 1.99.1) Suggests: RUnit, pasillaBamSubset, BiocManager License: GPL-3 Archs: x64 Package: traseR Version: 1.34.0 Depends: R (>= 3.5.0), GenomicRanges, IRanges, BSgenome.Hsapiens.UCSC.hg19 Suggests: BiocStyle,RUnit, BiocGenerics License: GPL Package: traviz Version: 1.10.0 Depends: R (>= 4.0) Imports: ggplot2, viridis, mgcv, SingleCellExperiment, slingshot, princurve, Biobase, methods, RColorBrewer, SummarizedExperiment, grDevices, graphics, rgl Suggests: scater, dplyr, testthat (>= 3.0.0), covr, S4Vectors, rmarkdown, knitr License: MIT + file LICENSE Package: TreeAndLeaf Version: 1.16.0 Depends: R(>= 4.0) Imports: RedeR(>= 1.40.4), igraph, ape Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr, geneplast, ggtree, ggplot2, dplyr, dendextend, RColorBrewer License: Artistic-2.0 Package: treeclimbR Version: 1.0.0 Depends: R (>= 4.4.0) Imports: TreeSummarizedExperiment (>= 1.99.0), edgeR, methods, SummarizedExperiment, S4Vectors, dirmult, dplyr, tibble, tidyr, ape, diffcyt, ggnewscale, ggplot2 (>= 3.4.0), viridis, ggtree, stats, utils, rlang Suggests: knitr, rmarkdown, scales, testthat (>= 3.0.0), BiocStyle License: Artistic-2.0 Package: treeio Version: 1.28.0 Depends: R (>= 3.6.0) Imports: ape, dplyr, jsonlite, magrittr, methods, rlang, stats, tibble, tidytree (>= 0.4.5), utils, yulab.utils (> 0.1.1) Suggests: Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml License: Artistic-2.0 Package: treekoR Version: 1.12.0 Depends: R (>= 4.1) Imports: stats, utils, tidyr, dplyr, data.table, ggiraph, ggplot2, hopach, ape, ggtree, patchwork, SingleCellExperiment, diffcyt, edgeR, lme4, multcomp Suggests: knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0) License: GPL-3 Package: TreeSummarizedExperiment Version: 2.12.0 Depends: R(>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18), Biostrings Imports: methods, BiocGenerics, utils, ape, rlang, dplyr, SummarizedExperiment, BiocParallel, IRanges, treeio Suggests: ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) Package: TREG Version: 1.8.0 Depends: R (>= 4.2), SummarizedExperiment Imports: Matrix, purrr, rafalib Suggests: BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap, sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0), tibble, tidyr, SingleCellExperiment License: Artistic-2.0 Package: Trendy Version: 1.26.0 Depends: R (>= 3.4) Imports: stats, utils, graphics, grDevices, segmented, gplots, parallel, magrittr, BiocParallel, DT, S4Vectors, SummarizedExperiment, methods, shiny, shinyFiles Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL-3 Package: TRESS Version: 1.10.0 Depends: R (>= 4.1.0), parallel, S4Vectors Imports: utils, rtracklayer, Matrix, matrixStats, stats, methods, graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools, AnnotationDbi Suggests: knitr, rmarkdown,BiocStyle License: GPL-3 + file LICENSE Package: tricycle Version: 1.12.0 Depends: R (>= 4.0), SingleCellExperiment Imports: methods, circular, ggplot2, ggnewscale, AnnotationDbi, scater, GenomicRanges, IRanges, S4Vectors, scattermore, dplyr, RColorBrewer, grDevices, stats, SummarizedExperiment, utils Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats, cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 Package: trigger Version: 1.50.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 Archs: x64 Package: trio Version: 3.42.0 Depends: R (>= 3.0.1) Imports: grDevices, graphics, methods, stats, survival, utils, siggenes, LogicReg (>= 1.6.1) Suggests: haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation License: LGPL-2 Package: triplex Version: 1.44.0 Depends: R (>= 2.15.0), S4Vectors (>= 0.5.14), IRanges (>= 2.5.27), XVector (>= 0.11.6), Biostrings (>= 2.39.10) Imports: methods, grid, GenomicRanges LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer License: BSD_2_clause + file LICENSE Archs: x64 Package: tripr Version: 1.10.0 Depends: shiny (>= 1.6.0), shinyBS Imports: shinyjs, shinyFiles, plyr, data.table, DT, stringr, stringdist, plot3D, gridExtra, RColorBrewer, plotly, dplyr, config (>= 0.3.1), golem (>= 0.3.1), methods, grDevices, graphics, stats, utils Suggests: BiocGenerics, shinycssloaders, tidyverse, BiocManager, Biostrings, xtable, rlist, motifStack, knitr, rmarkdown, testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis, pryr Enhances: parallel License: MIT + file LICENSE Package: tRNA Version: 1.22.0 Depends: R (>= 3.5), GenomicRanges, Structstrings Imports: stringr, S4Vectors, methods, BiocGenerics, IRanges, XVector, Biostrings, Modstrings, ggplot2, scales Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport License: GPL-3 + file LICENSE Package: tRNAdbImport Version: 1.22.0 Depends: R (>= 3.6), GenomicRanges, Modstrings, Structstrings, tRNA Imports: Biostrings, stringr, httr2, xml2, S4Vectors, methods, IRanges, utils Suggests: BiocGenerics, knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer License: GPL-3 + file LICENSE Package: tRNAscanImport Version: 1.24.0 Depends: R (>= 3.5), GenomicRanges, tRNA Imports: methods, stringr, BiocGenerics, Biostrings, Structstrings, S4Vectors, IRanges, XVector, GenomeInfoDb, rtracklayer, BSgenome, Rsamtools Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 + file LICENSE Package: TRONCO Version: 2.36.0 Depends: R (>= 4.1.0), Imports: bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel, iterators, RColorBrewer, circlize, igraph, grid, gridExtra, xtable, gtable, scales, R.matlab, grDevices, graphics, stats, utils, methods Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways, magick License: GPL-3 Package: TSAR Version: 1.2.0 Depends: R (>= 4.3.0) Imports: dplyr (>= 1.0.7), ggplot2 (>= 3.3.5), ggpubr (>= 0.4.0), magrittr (>= 2.0.3), mgcv (>= 1.8.38), readxl (>= 1.4.0), stringr (>= 1.4.0), tidyr (>= 1.1.4), utils (>= 4.3.1), shiny (>= 1.7.4.1), plotly (>= 4.10.2), shinyjs (>= 2.1.0), jsonlite (>= 1.8.7), rhandsontable (>= 0.3.8), openxlsx (>= 4.2.5.2), shinyWidgets (>= 0.7.6), minpack.lm (>= 1.2.3) Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 Package: TSCAN Version: 1.42.0 Depends: SingleCellExperiment, TrajectoryUtils Imports: ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, DelayedArray, S4Vectors Suggests: knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor License: GPL (>= 2) Package: ttgsea Version: 1.12.0 Depends: keras Imports: tm, text2vec, tokenizers, textstem, stopwords, data.table, purrr, DiagrammeR, stats Suggests: fgsea, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 Package: TTMap Version: 1.26.0 Depends: rgl, colorRamps Imports: grDevices,graphics,stats,utils, methods, SummarizedExperiment, Biobase Suggests: BiocStyle, airway License: GPL-2 Package: TurboNorm Version: 1.52.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: BiocStyle, affydata, hgu95av2cdf License: LGPL Archs: x64 Package: tweeDEseq Version: 1.50.0 Depends: R (>= 4.3.0) Imports: Rcpp (>= 1.0.10), MASS, limma, edgeR, parallel, cqn, grDevices, graphics, stats, utils LinkingTo: Rcpp Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) Archs: x64 Package: twilight Version: 1.80.0 Depends: R (>= 2.10), splines (>= 2.2.0), stats (>= 2.2.0), Biobase(>= 1.12.0) Imports: Biobase, graphics, grDevices, stats Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) License: GPL (>= 2) Archs: x64 Package: twoddpcr Version: 1.28.0 Depends: R (>= 3.4) Imports: class, ggplot2, hexbin, methods, scales, shiny, stats, utils, RColorBrewer, S4Vectors Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle License: GPL-3 Package: txcutr Version: 1.10.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, GenomicFeatures, txdbmaker, IRanges, GenomicRanges, BiocGenerics, Biostrings, S4Vectors, rtracklayer, BiocParallel, stats, methods, utils Suggests: RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown, testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 Package: txdbmaker Version: 1.0.1 Depends: BiocGenerics, S4Vectors, GenomeInfoDb (>= 1.39.9), GenomicRanges, GenomicFeatures Imports: methods, utils, stats, tools, httr, rjson, DBI, RSQLite (>= 2.0), IRanges, UCSC.utils, AnnotationDbi, Biobase, BiocIO, rtracklayer, biomaRt (>= 2.59.1) Suggests: RMariaDB, mirbase.db, ensembldb, RUnit, BiocStyle, knitr License: Artistic-2.0 Package: tximeta Version: 1.22.1 Imports: SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges, GenomicRanges, AnnotationDbi, GenomicFeatures, txdbmaker, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb, tools, utils, methods, Matrix Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, fishpond, edgeR, limma, devtools License: GPL-2 Package: tximport Version: 1.32.0 Imports: utils, stats, methods Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow, limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds License: LGPL (>= 2) Package: UCell Version: 2.8.0 Depends: R(>= 4.3.0) Imports: methods, data.table(>= 1.13.6), Matrix, stats, BiocParallel, BiocNeighbors, SingleCellExperiment, SummarizedExperiment Suggests: scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, Seurat(>= 5.0.0), SeuratObject(>= 5.0.0), knitr, rmarkdown License: GPL-3 + file LICENSE Package: UCSC.utils Version: 1.0.0 Imports: methods, stats, httr, jsonlite, S4Vectors Suggests: DBI, RMariaDB, GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 Package: Ularcirc Version: 1.22.0 Depends: R (>= 3.4.0) Imports: AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings, BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicAlignments, GenomicRanges, ggplot2, ggrepel, gsubfn, mirbase.db, moments, Organism.dplyr, plotgardener, R.utils, S4Vectors, shiny, shinydashboard, shinyFiles, shinyjs, yaml Suggests: BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE Package: uncoverappLib Version: 1.14.0 Imports: markdown, shiny, shinyjs, shinyBS, shinyWidgets,shinycssloaders, DT, Gviz, Homo.sapiens, openxlsx, condformat, stringr, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocFileCache,rappdirs, TxDb.Hsapiens.UCSC.hg19.knownGene, rlist, utils,S4Vectors, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, OrganismDbi, processx, Rsamtools, GenomicRanges Suggests: BiocStyle, knitr, testthat, rmarkdown, dplyr License: MIT + file LICENSE Package: UNDO Version: 1.46.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 Package: UniProt.ws Version: 2.44.0 Depends: BiocGenerics, methods, RSQLite, utils Imports: AnnotationDbi, BiocFileCache, BiocBaseUtils, httr, httpcache, jsonlite, progress, rjsoncons Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 Package: Uniquorn Version: 2.24.0 Depends: R (>= 3.5) Imports: stringr, R.utils, WriteXLS, stats, doParallel, foreach, GenomicRanges, IRanges, VariantAnnotation, data.table Suggests: testthat, knitr, rmarkdown, BiocGenerics License: Artistic-2.0 Package: universalmotif Version: 1.22.0 Depends: R (>= 3.5.0) Imports: methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp, Biostrings, BiocGenerics, S4Vectors, rlang, grid, MatrixGenerics LinkingTo: Rcpp, RcppThread Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio Enhances: PWMEnrich, rGADEM License: GPL-3 Archs: x64 Package: updateObject Version: 1.8.0 Depends: R (>= 4.2.0), methods, BiocGenerics (>= 0.47.1), S4Vectors Imports: utils, digest Suggests: GenomicRanges, SummarizedExperiment, InteractionSet, SingleCellExperiment, MultiAssayExperiment, TimiRGeN, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 Package: UPDhmm Version: 1.0.0 Depends: R (>= 4.3.0) Imports: HMM, utils, VariantAnnotation, GenomicRanges, S4Vectors, IRanges, stats Suggests: knitr, testthat (>= 2.1.0), BiocStyle, rmarkdown, markdown, karyoploteR, regioneR, dplyr License: MIT + file LICENSE Package: uSORT Version: 1.30.0 Depends: R (>= 3.3.0), tcltk Imports: igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr, methods, cluster, Biobase, fpc, BiocGenerics, monocle, grDevices, graphics, stats, utils Suggests: knitr, RUnit, testthat, ggplot2 License: Artistic-2.0 Package: VAExprs Version: 1.10.0 Depends: keras, mclust Imports: SingleCellExperiment, SummarizedExperiment, tensorflow, scater, CatEncoders, DeepPINCS, purrr, DiagrammeR, stats Suggests: SC3, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 Package: VanillaICE Version: 1.66.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>= 1.27.6), SummarizedExperiment (>= 1.5.3) Imports: MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges (>= 1.14.0), oligoClasses (>= 1.31.1), foreach, matrixStats, data.table, grid, lattice, methods, GenomeInfoDb (>= 1.11.4), crlmm, tools, stats, utils, BSgenome.Hsapiens.UCSC.hg18 Suggests: RUnit, human610quadv1bCrlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: LGPL-2 Archs: x64 Package: VarCon Version: 1.12.0 Depends: Biostrings, BSgenome, GenomicRanges, R (>= 4.1) Imports: methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2 Suggests: testthat, knitr, rmarkdown License: GPL-3 Package: variancePartition Version: 1.34.0 Depends: R (>= 4.3.0), ggplot2, limma, BiocParallel Imports: MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0), iterators, gplots, corpcor, matrixStats, RhpcBLASctl, reshape2, remaCor (>= 0.0.15), fANCOVA, aod, scales, Rdpack, rlang, lme4 (>= 1.1.33), grDevices, graphics, Biobase, methods, utils, stats Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, cowplot, Rfast, zenith, statmod, BiocGenerics, r2glmm, readr License: GPL-2 Package: VariantAnnotation Version: 1.50.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), MatrixGenerics, GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.19.5), Rsamtools (>= 2.19.1) Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.57.2), AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.39.7), BSgenome (>= 1.47.3), GenomicFeatures (>= 1.31.3) LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib (>= 2.99.0) Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle, knitr, magick, jsonlite, httr, rjsoncons License: Artistic-2.0 Archs: x64 Package: VariantFiltering Version: 1.40.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.25.1), VariantAnnotation (>= 1.13.29) Imports: utils, stats, Biobase, S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Biostrings (>= 2.33.11), GenomeInfoDb (>= 1.3.6), GenomicRanges (>= 1.19.13), SummarizedExperiment, GenomicFeatures, Rsamtools (>= 1.17.8), BSgenome, GenomicScores (>= 1.0.0), Gviz, shiny, shinythemes, shinyjs, DT, shinyTree LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 License: Artistic-2.0 Archs: x64 Package: VariantTools Version: 1.46.0 Depends: R (>= 3.5.0), S4Vectors (>= 0.17.33), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), VariantAnnotation (>= 1.11.16), methods Imports: Rsamtools (>= 1.31.2), BiocGenerics, Biostrings, parallel, GenomicFeatures (>= 1.31.3), Matrix, rtracklayer (>= 1.39.7), BiocParallel, GenomeInfoDb, BSgenome, Biobase Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3), TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: Artistic-2.0 Package: VaSP Version: 1.16.0 Depends: R (>= 4.0), ballgown Imports: IRanges, GenomicRanges, S4Vectors, parallel, matrixStats, GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats, graphics, methods Suggests: knitr, rmarkdown License: GPL (>= 2.0) Package: vbmp Version: 1.72.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) Package: VCFArray Version: 1.20.0 Depends: R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28) Imports: tools, GenomicRanges, VariantAnnotation (>= 1.29.3), GenomicFiles (>= 1.17.3), S4Vectors (>= 0.19.19), Rsamtools Suggests: SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown License: GPL-3 Package: VDJdive Version: 1.6.0 Depends: R (>= 4.2) Imports: BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix, methods, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, utils LinkingTo: Rcpp Suggests: breakaway, covr, knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 Archs: x64 Package: VegaMC Version: 3.42.0 Depends: R (>= 2.10.0), biomaRt, Biobase Imports: methods License: GPL-2 Archs: x64 Package: velociraptor Version: 1.14.3 Depends: SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, reticulate, S4Vectors, DelayedArray, basilisk, zellkonverter, scuttle, SingleCellExperiment, BiocParallel, BiocSingular Suggests: BiocStyle, testthat, knitr, rmarkdown, pkgdown, scran, scater, scRNAseq, Rtsne, graphics, grDevices, ggplot2, cowplot, GGally, patchwork, metR License: MIT + file LICENSE Package: veloviz Version: 1.10.0 Depends: R (>= 4.1) Imports: Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics, stats LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 Archs: x64 Package: VennDetail Version: 1.20.0 Imports: utils, grDevices, stats, methods, dplyr, purrr, tibble, magrittr, ggplot2, UpSetR, VennDiagram, grid, futile.logger Suggests: knitr, rmarkdown, testthat, markdown License: GPL-2 Package: VERSO Version: 1.14.0 Depends: R (>= 4.1.0) Imports: utils, data.tree, ape, parallel, Rfast, stats Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE Package: vidger Version: 1.24.0 Depends: R (>= 3.5) Imports: Biobase, DESeq2, edgeR, GGally, ggplot2, ggrepel, knitr, RColorBrewer, rmarkdown, scales, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, testthat License: GPL-3 | file LICENSE Package: viper Version: 1.38.0 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats, parallel, e1071, KernSmooth Suggests: bcellViper License: file LICENSE Package: ViSEAGO Version: 1.18.0 Depends: R (>= 3.6) Imports: data.table, AnnotationDbi, AnnotationForge, biomaRt, dendextend, DiagrammeR, DT, dynamicTreeCut, fgsea, GOSemSim, ggplot2, GO.db, grDevices, heatmaply, htmlwidgets, igraph, methods, plotly, processx, topGO, RColorBrewer, R.utils, scales, stats, UpSetR, utils Suggests: htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr, rmarkdown, corrplot, remotes, BiocManager Package: VisiumIO Version: 1.0.0 Depends: R (>= 4.4.0), TENxIO Imports: BiocBaseUtils, BiocGenerics, BiocIO, jsonlite, methods, S4Vectors, SpatialExperiment, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, tinytest License: Artistic-2.0 Package: vissE Version: 1.12.0 Depends: R (>= 4.1) Imports: igraph, methods, plyr, ggplot2, scico, RColorBrewer, tm, ggwordcloud, GSEABase, reshape2, grDevices, ggforce, msigdb, ggrepel, textstem, tidygraph, stats, scales, ggraph Suggests: testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore, knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr License: GPL-3 Package: Voyager Version: 1.6.0 Depends: R (>= 4.2.0), SpatialFeatureExperiment (>= 1.5.2) Imports: BiocParallel, bluster, ggnewscale, ggplot2 (>= 3.4.0), grDevices, grid, lifecycle, Matrix, matrixStats, memuse, methods, patchwork, rlang, RSpectra, S4Vectors, scales, scico, sf, SingleCellExperiment, SpatialExperiment, spdep, stats, SummarizedExperiment, terra, utils Suggests: automap, BiocSingular, BiocStyle, cowplot, EBImage, ExperimentHub, ggh4x, gstat, hexbin, knitr, pheatmap, RBioFormats, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, vroom, xml2 License: Artistic-2.0 Package: VplotR Version: 1.14.0 Depends: R (>= 4.0), GenomicRanges, IRanges, ggplot2 Imports: cowplot, magrittr, GenomeInfoDb, GenomicAlignments, RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2, methods, graphics, stats Suggests: GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown License: GPL (>= 3) Package: vsclust Version: 1.6.0 Depends: R (>= 4.2.0) Imports: matrixStats, limma, parallel, shiny, qvalue, grDevices, stats, MultiAssayExperiment, graphics LinkingTo: Rcpp Suggests: knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, clusterProfiler License: GPL-2 Archs: x64 Package: vsn Version: 3.72.0 Depends: R (>= 4.0.0), methods, Biobase Imports: affy, limma, lattice, ggplot2 Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat License: Artistic-2.0 Archs: x64 Package: vtpnet Version: 0.44.0 Depends: R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel, foreach Suggests: MotifDb, VariantAnnotation, Rgraphviz License: Artistic-2.0 Package: vulcan Version: 1.26.0 Depends: R (>= 4.0), ChIPpeakAnno,TxDb.Hsapiens.UCSC.hg19.knownGene, zoo, GenomicRanges, S4Vectors, viper, DiffBind, locfit Imports: wordcloud, csaw, gplots, stats, utils, caTools, graphics, DESeq2, Biobase Suggests: vulcandata License: LGPL-3 Package: wateRmelon Version: 2.10.0 Depends: R (>= 3.5.0), Biobase, limma, methods, matrixStats, methylumi, lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19, illuminaio Imports: Biobase Suggests: RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BiocStyle, knitr, rmarkdown, IlluminaHumanMethylationEPICmanifest, irlba, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore Enhances: minfi License: GPL-3 Package: wavClusteR Version: 2.38.0 Depends: R (>= 3.2), GenomicRanges (>= 1.31.8), Rsamtools Imports: methods, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Biostrings (>= 2.47.6), foreach, GenomicFeatures (>= 1.31.3), ggplot2, Hmisc, mclust, rtracklayer (>= 1.39.7), seqinr, stringr Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 Enhances: doMC License: GPL-2 Package: weaver Version: 1.70.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools License: GPL-2 Package: webbioc Version: 1.76.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: multtest, qvalue, stats, utils, BiocManager License: GPL (>= 2) Package: weitrix Version: 1.16.0 Depends: R (>= 3.6), SummarizedExperiment Imports: methods, utils, stats, grDevices, assertthat, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocGenerics, limma, topconfects, dplyr, purrr, ggplot2, rlang, scales, reshape2, splines, Ckmeans.1d.dp, glm2, RhpcBLASctl Suggests: knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR, EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, ComplexHeatmap, patchwork, testthat (>= 2.1.0) License: LGPL-2.1 | file LICENSE Package: widgetTools Version: 1.82.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL Package: wiggleplotr Version: 1.28.0 Depends: R (>= 3.6) Imports: dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer, cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb Suggests: knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter License: Apache License 2.0 Package: wpm Version: 1.14.0 Depends: R (>= 4.1.0) Imports: utils, methods, cli, Biobase, SummarizedExperiment, config, golem, shiny, DT, ggplot2, dplyr, rlang, stringr, shinydashboard, shinyWidgets, shinycustomloader, RColorBrewer, logging Suggests: MSnbase, testthat, BiocStyle, knitr, rmarkdown License: Artistic-2.0 Package: wppi Version: 1.12.0 Depends: R(>= 4.1) Imports: dplyr, igraph, logger, methods, magrittr, Matrix, OmnipathR(>= 2.99.8), progress, purrr, rlang, RCurl, stats, tibble, tidyr Suggests: knitr, testthat, rmarkdown License: MIT + file LICENSE Package: Wrench Version: 1.22.0 Depends: R (>= 3.5.0) Imports: limma, matrixStats, locfit, stats, graphics Suggests: knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR License: Artistic-2.0 Package: xcms Version: 4.2.2 Depends: R (>= 4.0.0), BiocParallel (>= 1.8.0) Imports: MSnbase (>= 2.29.3), mzR (>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics (>= 1.35.4), lattice, MassSpecWavelet (>= 1.66.0), S4Vectors, IRanges, SummarizedExperiment, MsCoreUtils (>= 1.15.5), MsFeatures, MsExperiment (>= 1.5.4), Spectra (>= 1.13.7), progress, jsonlite, RColorBrewer, MetaboCoreUtils (>= 1.11.2) Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>= 0.25.1), ncdf4, testthat (>= 3.1.9), pander, rmarkdown, MALDIquant, pheatmap, RANN, multtest, MsBackendMgf, signal, mgcv Enhances: Rgraphviz, rgl License: GPL (>= 2) + file LICENSE Archs: x64 Package: xcore Version: 1.8.0 Depends: R (>= 4.2) Imports: DelayedArray (>= 0.18.0), edgeR (>= 3.34.1), foreach (>= 1.5.1), GenomicRanges (>= 1.44.0), glmnet (>= 4.1.2), IRanges (>= 2.26.0), iterators (>= 1.0.13), magrittr (>= 2.0.1), Matrix (>= 1.3.4), methods (>= 4.1.1), MultiAssayExperiment (>= 1.18.0), stats, S4Vectors (>= 0.30.0), utils Suggests: AnnotationHub (>= 3.0.2), BiocGenerics (>= 0.38.0), BiocParallel (>= 1.28), BiocStyle (>= 2.20.2), data.table (>= 1.14.0), devtools (>= 2.4.2), doParallel (>= 1.0.16), ExperimentHub (>= 2.2.0), knitr (>= 1.37), pheatmap (>= 1.0.12), proxy (>= 0.4.26), ridge (>= 3.0), rmarkdown (>= 2.11), rtracklayer (>= 1.52.0), testthat (>= 3.0.0), usethis (>= 2.0.1), xcoredata License: GPL-2 Package: XDE Version: 2.50.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5) Imports: BiocGenerics, genefilter, graphics, grDevices, gtools, methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta, siggenes Suggests: MASS, RUnit Enhances: coda License: LGPL-2 Archs: x64 Package: Xeva Version: 1.20.0 Depends: R (>= 3.6) Imports: methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2, scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid, nlme, PharmacoGx, downloader Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 Package: XINA Version: 1.22.0 Depends: R (>= 3.5) Imports: mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools, grDevices, graphics, utils, STRINGdb Suggests: knitr, rmarkdown License: GPL-3 Package: xmapbridge Version: 1.62.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 Package: XNAString Version: 1.12.0 Depends: R (>= 4.1) Imports: utils, Biostrings, pwalign, BSgenome, data.table, GenomicRanges, IRanges, methods, Rcpp, stringi, S4Vectors, future.apply, stringr, formattable, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat, BSgenome.Hsapiens.UCSC.hg38, pander License: GPL-2 Archs: x64 Package: XVector Version: 0.44.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9) Imports: methods, utils, tools, zlibbioc, BiocGenerics, S4Vectors, IRanges LinkingTo: S4Vectors, IRanges Suggests: Biostrings, drosophila2probe, RUnit License: Artistic-2.0 Archs: x64 Package: yamss Version: 1.30.0 Depends: R (>= 4.3.0), methods, BiocGenerics (>= 0.15.3), SummarizedExperiment Imports: IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table, grDevices, limma Suggests: BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat License: Artistic-2.0 Package: YAPSA Version: 1.30.0 Depends: R (>= 4.0.0), GenomicRanges, ggplot2, grid Imports: limSolve, SomaticSignatures, VariantAnnotation, GenomeInfoDb, reshape2, gridExtra, corrplot, dendextend, GetoptLong, circlize, gtrellis, doParallel, parallel, PMCMRplus, ggbeeswarm, ComplexHeatmap, KEGGREST, grDevices, Biostrings, BSgenome.Hsapiens.UCSC.hg19, magrittr, pracma, dplyr, utils Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL-3 Package: yarn Version: 1.30.0 Depends: Biobase Imports: biomaRt, downloader, edgeR, gplots, graphics, limma, matrixStats, preprocessCore, readr, RColorBrewer, stats, quantro Suggests: knitr, rmarkdown, testthat (>= 0.8) License: Artistic-2.0 Package: zellkonverter Version: 1.14.1 Imports: Matrix, basilisk, reticulate, SingleCellExperiment (>= 1.11.6), SummarizedExperiment, DelayedArray, methods, S4Vectors, utils, cli Suggests: anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rmarkdown, rhdf5 (>= 2.45.1), scRNAseq, spelling, testthat, withr License: MIT + file LICENSE Package: zenith Version: 1.6.0 Depends: R (>= 4.2.0), limma, methods Imports: variancePartition (>= 1.26.0), EnrichmentBrowser (>= 2.22.0), GSEABase (>= 1.54.0), msigdbr (>= 7.5.1), Rfast, ggplot2, tidyr, reshape2, progress, utils, Rdpack, stats Suggests: BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit License: Artistic-2.0 Package: zFPKM Version: 1.26.0 Depends: R (>= 3.4.0) Imports: checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment Suggests: knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown License: GPL-3 | file LICENSE Package: zinbwave Version: 1.26.0 Depends: R (>= 3.4), methods, SummarizedExperiment, SingleCellExperiment Imports: BiocParallel, softImpute, stats, genefilter, edgeR, Matrix Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, sparseMatrixStats License: Artistic-2.0 Package: zlibbioc Version: 1.50.0 Suggests: BiocStyle, knitr License: Artistic-2.0 + file LICENSE Archs: x64 Package: ZygosityPredictor Version: 1.4.0 Depends: R (>= 4.3.0) Imports: GenomicAlignments, GenomicRanges, Rsamtools, IRanges, VariantAnnotation, DelayedArray, dplyr, stringr, purrr, tibble, methods, knitr, igraph, readr, stats, magrittr, rlang Suggests: rmarkdown, testthat, BiocStyle License: GPL-2