edgeR is an R package used to analyze replicated count-based expression data. Briefly, edgeR estimates the genewise dispersions by conditional maximum likelihood, conditioning on the total count for that gene. An empirical Bayes procedure is used to shrink the dispersions towards a consensus value, effectively borrowing information between genes. Finally, differential expression is assessed for each gene using an exact test analogous to Fisher's exact test, but adapted for overdispersed data. For more information on how to install this package click here.

References:

Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics (Oxford, England), 26(1), 139–140. https://doi.org/10.1093/bioinformatics/btp616

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