edgeR
This is the development version of edgeR; for the stable release version, see edgeR.
Empirical Analysis of Digital Gene Expression Data in R
Bioconductor version: Development (3.23)
Differential expression analysis of sequence count data. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models, quasi-likelihood, and gene set enrichment. Can perform differential analyses of any type of omics data that produces read counts, including RNA-seq, ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE, CAGE, metabolomics, or proteomics spectral counts. RNA-seq analyses can be conducted at the gene or isoform level, and tests can be conducted for differential exon or transcript usage.
Author: Yunshun Chen, Lizhong Chen, Aaron TL Lun, Davis J McCarthy, Pedro Baldoni, Matthew E Ritchie, Belinda Phipson, Yifang Hu, Xiaobei Zhou, Mark D Robinson, Gordon K Smyth
Maintainer: Yunshun Chen <yuchen at wehi.edu.au>, Gordon Smyth <smyth at wehi.edu.au>, Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>, Mark Robinson <mark.robinson at imls.uzh.ch>
citation("edgeR")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("edgeR")
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("edgeR")| A brief introduction to edgeR | HTML | R Script |
| edgeR User's Guide | ||
| Reference Manual |
Details
| biocViews | AlternativeSplicing, BatchEffect, Bayesian, BiomedicalInformatics, CellBiology, ChIPSeq, Clustering, Coverage, DNAMethylation, DifferentialExpression, DifferentialMethylation, DifferentialSplicing, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, MultipleComparison, Normalization, Pathways, Proteomics, QualityControl, RNASeq, Regression, SAGE, Sequencing, SingleCell, Software, SystemsBiology, TimeCourse, Transcription, Transcriptomics |
| Version | 4.9.0 |
| In Bioconductor since | BioC 2.3 (R-2.8) (17 years) |
| License | GPL (>=2) |
| Depends | R (>= 3.6.0), limma(>= 3.63.6) |
| Imports | methods, graphics, stats, utils, locfit |
| System Requirements | |
| URL | https://bioinf.wehi.edu.au/edgeR/ https://bioconductor.org/packages/edgeR |
See More
| Suggests | arrow, jsonlite, knitr, Matrix, readr, rhdf5, SeuratObject, splines, AnnotationDbi, Biobase, BiocStyle, org.Hs.eg.db, SummarizedExperiment |
| Linking To | |
| Enhances | |
| Depends On Me | methylMnM, ReactomeGSA.data, EGSEA123, RNAseq123, rnaseqDTU, RnaSeqGeneEdgeRQL, csawBook, OSCA.advanced, OSCA.multisample, OSCA.workflows, babel, BALLI, BioInsight, SCdeconR |
| Imports Me | AWFisher, compcodeR, erccdashboard, MetaDICT, ppcseq, PROPER, RNAseqCovarImpute, ROSeq, Rvisdiff, scde, SIMD, tweeDEseq, spatialLIBD, ExpHunterSuite, recountWorkflow, aIc, bulkAnalyseR, CAMML, cinaR, CoreMicrobiomeR, cpam, hicream, HTSCluster, idiffomix, microbial, RCPA, RVA, scITD, scRNAtools, ssizeRNA, TransProR, TSGS |
| Suggests Me | ABSSeq, biobroom, cqn, dcanr, dearseq, easyreporting, subSeq, tximport, variancePartition, Wrench, CAGEWorkflow, chipseqDB, DGEobj, DGEobj.utils, DiPALM, easybio, ggpicrust2, glmmSeq, inDAGO, MiscMetabar, palasso, pctax, pmartR, seqgendiff, SIBERG, volcano3D |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | edgeR_4.9.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/edgeR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/edgeR |
| Bioc Package Browser | https://code.bioconductor.org/browse/edgeR/ |
| Package Short Url | https://bioconductor.org/packages/edgeR/ |
| Package Downloads Report | Download Stats |