Is there an R statistical program for calculating differential gene expression with paired RNA-seq data?

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Steffen Priebe

This should be possible using generalized linear models. There are used in the new version of DESeq (DESeq2) and edgeR.

See section 5.4 in the DESeq manual:

http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.pdf

Aliaksei Z Holik

To supplement Steffen's answer, here's the link to edgeR manual. Chapter 3.4 describes the paired design.

http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf