methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Perl is needed to read SAM files only.
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install bioconductor-methylkit
and update with:
conda update bioconductor-methylkit
A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-methylkit.