recipe bioconductor-methylkit

DNA methylation analysis from high-throughput bisulfite sequencing results

Homepage

https://bioconductor.org/packages/3.10/bioc/html/methylKit.html

License

Artistic-2.0

Recipe

/bioconductor-methylkit/meta.yaml

Links

biotools: 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.

package bioconductor-methylkit

Versions

1.12.0-0, 1.10.0-1, 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 >=1.32.0,<1.33.0

• bioconductor-genomeinfodb >=1.22.0,<1.23.0

• bioconductor-genomicranges >=1.38.0,<1.39.0

• bioconductor-iranges >=2.20.0,<2.21.0

• bioconductor-limma >=3.42.0,<3.43.0

• bioconductor-qvalue >=2.18.0,<2.19.0

• bioconductor-rhtslib >=1.18.0,<1.19.0

• bioconductor-rsamtools >=2.2.0,<2.3.0

• bioconductor-rtracklayer >=1.46.0,<1.47.0

• bioconductor-s4vectors >=0.24.0,<0.25.0

• bioconductor-zlibbioc >=1.32.0,<1.33.0

• libgcc-ng >=7.3.0

• libstdcxx-ng >=7.3.0

• r-base >=3.6,<3.7.0a0

• r-data.table >=1.9.6

• r-emdbook

• r-gtools

• r-kernsmooth

• r-mclust

• r-mgcv

• r-r.utils

• r-rcpp

Required By

• bioconductor-methinheritsim

• bioconductor-methcp

• bioconductor-methylinheritance

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>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-methylkit/README.html)