lovivi / ComBat-seq

Batch effect adjustment algorithm based on Negative Binomial regression for sequencing read counts

About ComBat-seq

ComBat-seq is a batch effect adjustment (BEA) tool for RNA-seq read counts, using Negative Binomial regression. To use it, download the ComBat_seq.R and helper_seq.R scripts, and run the function with the syntax below:

source("ComBat_seq.R")
source("helper_seq.R")
# include condition (group variable)
adjusted_counts <- ComBat_seq(count_matrix, batch=batch, group=group, full_mod=TRUE)
# do not include condition
adjusted_counts <- ComBat_seq(count_matrix, batch=batch, group=NULL, full_mod=FALSE)