BSmooth is a pipeline for analyzing whole genome bisulfite sequencing
(WGBS) data. It includes tools for aligning the data, quality
control, and identifying differentially methylated regions (DMRs).
- bsmooth-align (version 0.8.1).
This integrates two different pipelines for aligning WGBS data. One
of the alignment tools, Merman, is included in the archive. The other
alignment tool, Bowtie 2, must be downloaded and installed separately.
Bowtie 2 version 2.0.5 or later is needed. See included README
file for details on how to install. This project is also
- bsseq (version 0.4.2). This is a R
package used for smoothing methylation profiles and identifying DMRs.
The starting point is a (matrix) of U and M values. The package
contains two vignettes (manuals), one of which contains an analysis of
a real dataset. The package is now available on Bioconductor, and we
strongly encourage users to obtain it there. This version requires
R-2.15 or greater.
- bsseqData (version 0.1.1). This is
an experiment data package for R, containing an example dataset used
in the vignettes (chromosome 21 and 22 from 3 normal colon and 3 colon