tweeDEseq: analysis of RNA-seq data using the Poisson-Tweedie family of distributions

This document gives an overview of the R package tweeDEseq, which provides statistical procedures for testing differential expression in RNA-seq count data. In fact, these procedures could be applied, in principle, to any kind of count data, other than RNA-seq. The tweeDEseq package offers a function for normalizing count data which actually calls other functions for that purpose from the edgeR package. For this reason, it is necessary to have installed the edgeR package as well, although it is not necessary to explicitly load it onto the session. Another package necessary for running this vignette is the tweeDEseqCountData package which contains data to illustrate the analyses and which is employed in the article introducing tweeDEseq by Esnaola et al. (2011). Therefore, we should start the R session with loading these libraries as follows: