MethylSig is our new R package for analyzing whole-genome bisulfite sequencing (bis-seq), reduced representation bisulfite sequencing (RRBS), or enhanced RRBS experiments. Methylsig tests for differentially methylated sites (DMCs) or regions (DMRs) using a beta-binomial model to account for the coverage and variation among samples at each CpG site or region, and has a well-calibrated Type 1 error rate. Several options exist for either site-specific or sliding window tests, combining strands, filtering sites, and for local variance estimation. In addition, methylSig offers numerous functions for annotating and visualizing results, and testing for enrichment of overlap with the binding sites of transcription factors.
Check out methylSig on GitHub

The easiest way to install methylSig is with the devtools R package:

> library(devtools) 
> install_github('sartorlab/methylSig')

methylSig vignette: methylSig.pdf

ENCODE tfbs annotation files:

hg18: ENCODE_YaleTfbs.hg18.txt.gz
hg19: ENCODE_AwgTfbs.hg19.txt.gz
mm9: ENCODE_Tfbs.mm9.txt.gz