GRaNIE
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see GRaNIE.
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data
Bioconductor version: 3.16
Genetic variants associated with diseases often affect non-coding regions, thus likely having a regulatory role. To understand the effects of genetic variants in these regulatory regions, identifying genes that are modulated by specific regulatory elements (REs) is crucial. The effect of gene regulatory elements, such as enhancers, is often cell-type specific, likely because the combinations of transcription factors (TFs) that are regulating a given enhancer have celltype specific activity. This TF activity can be quantified with existing tools such as diffTF and captures differences in binding of a TF in open chromatin regions. Collectively, this forms a gene regulatory network (GRN) with cell-type and data-specific TF-RE and RE-gene links. Here, we reconstruct such a GRN using bulk RNAseq and open chromatin (e.g., using ATACseq or ChIPseq for open chromatin marks) and optionally TF activity data. Our network contains different types of links, connecting TFs to regulatory elements, the latter of which is connected to genes in the vicinity or within the same chromatin domain (TAD). We use a statistical framework to assign empirical FDRs and weights to all links using a permutation-based approach.
Author: Christian Arnold [cre, aut], Judith Zaugg [aut], Rim Moussa [aut], Armando Reyes-Palomares [ctb], Giovanni Palla [ctb], Maksim Kholmatov [ctb]
Maintainer: Christian Arnold <chrarnold at web.de>
citation("GRaNIE")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GRaNIE")
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("GRaNIE")| Package Details | HTML | R Script |
| Workflow example | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, BiomedicalInformatics, ChIPSeq, GeneExpression, GeneRegulation, GeneSetEnrichment, Genetics, GraphAndNetwork, NetworkInference, RNASeq, Regression, Software, Transcription, Transcriptomics |
| Version | 1.2.7 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2.0) |
| Imports | futile.logger, checkmate, patchwork, reshape2, data.table, matrixStats, Matrix, GenomicRanges, RColorBrewer, ComplexHeatmap, DESeq2, circlize, progress, utils, methods, stringr, 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 |
| System Requirements | |
| URL | https://grp-zaugg.embl-community.io/GRaNIE |
| Bug Reports | https://git.embl.de/grp-zaugg/GRaNIE/issues |
See More
| 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, 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, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, IHW, clusterProfiler, ReactomePA, DOSE, BiocFileCache, ChIPseeker, testthat (>= 3.0.0), BiocStyle, csaw, BiocParallel, robust, variancePartition, purrr, EDASeq, JASPAR2022, TFBSTools, motifmatchr, rbioapi |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GRaNIE_1.2.7.tar.gz |
| Windows Binary | GRaNIE_1.2.7.zip (64-bit only) |
| macOS Binary (x86_64) | GRaNIE_1.2.7.tgz |
| macOS Binary (arm64) | GRaNIE_1.2.7.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GRaNIE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GRaNIE |
| Bioc Package Browser | https://code.bioconductor.org/browse/GRaNIE/ |
| Package Short Url | https://bioconductor.org/packages/GRaNIE/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |