recipe bioconductor-methylkit

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. Methylation calling can be performed directly from Bismark aligned BAM files.







biotools: methylkit

package bioconductor-methylkit

(downloads) docker_bioconductor-methylkit


1.8.1-0, 1.8.0-0, 1.6.3-0, 1.4.0-0, 1.2.4-0, 1.0.0-0, 0.99.2-0

Depends bioconductor-fastseg


Depends bioconductor-genomeinfodb


Depends bioconductor-genomicranges


Depends bioconductor-iranges


Depends bioconductor-limma


Depends bioconductor-qvalue


Depends bioconductor-rhtslib


Depends bioconductor-rsamtools


Depends bioconductor-rtracklayer


Depends bioconductor-s4vectors


Depends bioconductor-zlibbioc


Depends libgcc-ng


Depends libstdcxx-ng


Depends r-base


Depends r-data.table


Depends r-emdbook

Depends r-gtools

Depends r-kernsmooth

Depends r-mclust

Depends r-r.utils

Depends r-rcpp



With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-methylkit

and update with:

conda update bioconductor-methylkit

or use the docker container:

docker pull<tag>

(see bioconductor-methylkit/tags for valid values for <tag>)