Package: edgeR
Version: 4.6.3
Date: 2025-07-05
Title: Empirical Analysis of Digital Gene Expression Data in R
Description: 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@wehi.edu.au>, Gordon Smyth <smyth@wehi.edu.au>,
 Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>,
 Mark Robinson <mark.robinson@imls.uzh.ch>
License: GPL (>=2)
Depends: R (>= 3.6.0), limma (>= 3.63.6)
Imports: methods, graphics, stats, utils, locfit
Suggests: arrow, jsonlite, knitr, Matrix, readr, rhdf5, SeuratObject,
        splines, AnnotationDbi, Biobase, BiocStyle, org.Hs.eg.db,
        SummarizedExperiment
VignetteBuilder: knitr
URL: https://bioinf.wehi.edu.au/edgeR/,
        https://bioconductor.org/packages/edgeR
biocViews: AlternativeSplicing, BatchEffect, Bayesian,
        BiomedicalInformatics, CellBiology, ChIPSeq, Clustering,
        Coverage, DifferentialExpression, DifferentialMethylation,
        DifferentialSplicing, DNAMethylation, Epigenetics,
        FunctionalGenomics, GeneExpression, GeneSetEnrichment,
        Genetics, Genetics, ImmunoOncology, MultipleComparison,
        Normalization, Pathways, Proteomics, QualityControl,
        Regression, RNASeq, SAGE, Sequencing, SingleCell,
        SystemsBiology, TimeCourse, Transcription, Transcriptomics
NeedsCompilation: yes
git_url: https://git.bioconductor.org/packages/edgeR
git_branch: RELEASE_3_21
git_last_commit: 0dc836a
git_last_commit_date: 2025-07-04
Repository: Bioconductor 3.21
Date/Publication: 2025-07-07
Packaged: 2025-07-07 22:44:22 UTC; biocbuild
Built: R 4.5.1; x86_64-apple-darwin20; 2025-07-08 16:56:40 UTC; unix
