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.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/methylKit.html

License

Artistic-2.0

Recipe

/bioconductor-methylkit/meta.yaml

Links

biotools: methylkit

package bioconductor-methylkit

(downloads) docker_bioconductor-methylkit

Versions

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

>=1.28.0,<1.29.0

Depends bioconductor-genomeinfodb

>=1.18.0,<1.19.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-iranges

>=2.16.0,<2.17.0

Depends bioconductor-limma

>=3.38.0,<3.39.0

Depends bioconductor-qvalue

>=2.14.0,<2.15.0

Depends bioconductor-rhtslib

>=1.14.0,<1.15.0

Depends bioconductor-rsamtools

>=1.34.0,<1.35.0

Depends bioconductor-rtracklayer

>=1.42.0,<1.43.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends bioconductor-zlibbioc

>=1.28.0,<1.29.0

Depends libgcc-ng

>=7.3.0

Depends libstdcxx-ng

>=7.3.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-data.table

>=1.9.6

Depends r-emdbook

Depends r-gtools

Depends r-kernsmooth

Depends r-mclust

Depends r-r.utils

Depends r-rcpp

Requirements

Installation

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 quay.io/biocontainers/bioconductor-methylkit:<tag>

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