baySeq is a package for calculating Differential Expression in Solexa-type, or count, data for the R Project For Statistical Computing. It was previously available on these pages but is now part of Bioconductor. For more information please see the Bioconductor website.
For details on the methods being used, consult Hardcastle et al. (2009) Empirical Bayesian methods for estimating differential expression in count data.