Within the last couple of weeks, the bsseq package (new) was added to the devel repository, http://bioconductor.org/packages/2.11/bioc/html/bsseq.html This package is used for the analysis of whole-genome bisulfite sequencing data, used for studying DNA methylation. The package contains the reference implementation of the non-alignment portion of the BSmooth algorithm, first used in Hansen, K. D. et al. Increased methylation variation in epigenetic domains across cancer types. Nat Genet 43, 768?775 (2011). and better described in Hansen, K.D. et al. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biology, in press (2012). The remaining part of BSmooth (the alignment suite) can be obtained from http://rafalab.jhsph.edu/bsmooth/ In addition to the implementation of the main statistical algorithm, the package contains tools for handling and manipulating whole-genome bisulfite sequencing data. We have also used these tools to handle capture (targetted) bisulfite sequencing, although the statistical algorithm (BSmooth) does not handle such data out of the box. The parallel package is used to support parallel computing across multiple cores in a single node. In order to handle human genome wide data, you will need access to a machine with a reasonable amount of RAM (say 32GB). The package contains two vignettes, including one that contains a rough analysis of a 3 vs 3 colon cancer data on chr21 and chr22 from the first publication above. This data is contained in the experimental package bsseqData. The vignette(s) contains more detail on limitations of the package. While the package is new on Bioconductor, we have been using earlier versions internally for quite a while. The most recent changes (for people who may have had access to earlier versions) include vastly improved documentation. Best, Kasper D Hansen