recipe bioconductor-methylkit

DNA methylation analysis from high-throughput bisulfite sequencing results

Homepage

https://bioconductor.org/packages/3.11/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

1.14.1-0,  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, 

1.14.1-0,  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 >=1.34.0,<1.35.0

• bioconductor-genomeinfodb >=1.24.0,<1.25.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-limma >=3.44.0,<3.45.0

• bioconductor-qvalue >=2.20.0,<2.21.0

• bioconductor-rhtslib >=1.20.0,<1.21.0

• bioconductor-rsamtools >=2.4.0,<2.5.0

• bioconductor-rtracklayer >=1.48.0,<1.49.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-zlibbioc >=1.34.0,<1.35.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=7.3.0

• liblapack >=3.8.0,<3.9.0a0

• libstdcxx-ng >=7.3.0

• r-base >=4.0,<4.1.0a0

• r-data.table >=1.9.6

• r-emdbook

• r-gtools

• r-kernsmooth

• r-mclust

• r-mgcv

• r-r.utils

• r-rcpp

Required By

• bioconductor-methylinheritance

• bioconductor-methinheritsim

• bioconductor-methcp

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)