singleCellTK

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see singleCellTK.

Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data


Bioconductor version: 3.13

Run common single cell analysis in the R console or directly through your browser. Includes many functions for import, quality control, normalization, batch correction, clustering, differential expression, and visualization..

Author: David Jenkins [aut] , Vidya Akavoor [aut], Salam Alabdullatif [aut], Shruthi Bandyadka [aut], Emma Briars [aut] , Xinyun Cao [aut], Sebastian Carrasco Pro [aut], Tyler Faits [aut], Rui Hong [aut], Mohammed Muzamil Khan [aut], Yusuke Koga [aut, cre], Anastasia Leshchyk [aut], Irzam Sarfraz [aut], Yichen Wang [aut], Zhe Wang [aut], W. Evan Johnson [aut] , Joshua David Campbell [aut]

Maintainer: Yusuke Koga <ykoga07 at bu.edu>

Citation (from within R, enter citation("singleCellTK")):

Installation

To install this package, start R (version "4.1") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("singleCellTK")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("singleCellTK")
1. Introduction to singleCellTK HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Alignment, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, SingleCell, Software
Version 2.2.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License MIT + file LICENSE
Depends R (>= 4.0), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase
Imports ape, batchelor, BiocParallel, celldex, colourpicker, colorspace, cowplot, cluster, ComplexHeatmap, data.table, DelayedMatrixStats, DESeq2, dplyr, DT, ExperimentHub, fields, ggplot2, ggplotify, ggrepel, ggtree, gridExtra, GSVA(>= 1.26.0), GSVAdata, igraph, KernSmooth, limma, MAST, Matrix, matrixStats, methods, msigdbr, multtest, plotly, RColorBrewer, ROCR, Rtsne, S4Vectors, scater, scMerge(>= 1.2.0), scran, Seurat (>= 3.1.3), shiny, shinyjs, SingleR, sva, reshape2, AnnotationDbi, shinyalert, circlize, enrichR, celda, shinycssloaders, uwot, DropletUtils, scds(>= 1.2.0), reticulate (>= 1.14), tools, tximport, fishpond, withr, GSEABase, R.utils, zinbwave, scRNAseq(>= 2.0.2), TENxPBMCData, yaml, rmarkdown, magrittr, scDblFinder, metap
System Requirements
URL https://compbiomed.github.io/sctk_docs/
Bug Reports https://github.com/compbiomed/singleCellTK/issues
See More
Suggests testthat, Rsubread, BiocStyle, knitr, lintr, xtable, spelling, org.Mm.eg.db, stringr, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me celda
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package singleCellTK_2.2.0.tar.gz
Windows Binary singleCellTK_2.2.0.zip
macOS 10.13 (High Sierra) singleCellTK_2.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/singleCellTK
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/singleCellTK
Bioc Package Browser https://code.bioconductor.org/browse/singleCellTK/
Package Short Url https://bioconductor.org/packages/singleCellTK/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.13 Source Archive