domain/differential-expression

Detection and accurate false discovery rate control of differentially methylated regions from whole genome bisulfite sequencing

ComBat-seq: batch effect adjustment for RNA-seq count data

DESeq2 vignette — "Analyzing RNA-seq data with DESeq2"

limma: Linear Models for Microarray and Omics Data — package documentation

RNA-seq workflow: gene-level exploratory analysis and differential expression (rnaseqGene)

The SVA package for removing batch effects and other unwanted variation in high-throughput experiments

High-Throughput Count Data and Generalized Linear Models