MethylKit is an R package for DNA methylation analysis from high-throughput bisulfite sequencing. It has many features, coverage/methylation statistics, differential methylation analysis, feature annotation, reading methylation calls.
Normally, bisulfite converted reads are aligned to the genome and % methylation value per base is calculated.
Methylkit takes those percentages as its input. (It can be taken by using their RRBS pipeline or other inputs such as a tab-delimited file, BSMAP methylation ratio files, or sorted SAM files.