edgeR

Empirical Analysis of Digital Gene Expression Data in R

Bioconductor version: 3.23 · Package version: 4.10.1

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.

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

BiocManager::install("edgeR")