Package: edgeR
Version: 4.99.11
Date: 2026-10-31
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>
License: GPL (>=2)
Depends: R (>= 3.6.0), limma (>= 3.63.6)
Imports: methods, graphics, stats, utils
Suggests: jsonlite, knitr, Matrix, nanoparquet, readr, rhdf5,
        SeuratObject, splines, AnnotationDbi, Biobase, BiocStyle,
        org.Hs.eg.db, S4Vectors, 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
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-31 21:11:33 UTC
RemoteUrl: https://github.com/bioc/edgeR
RemoteRef: HEAD
RemoteSha: c708c74473eb7781078133cb51a4f0ffa77f3b67
Packaged: 2026-10-31 22:26:08 UTC; root