recipe bioconductor-charm

This package implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. It finds differentially methylated regions between samples, calculates percentage methylation estimates and includes array quality assessment tools.

Homepage

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

License

LGPL (>= 2)

Recipe

/bioconductor-charm/meta.yaml

package bioconductor-charm

Versions

2.28.0-0

Depends

• bioconductor-biobase >=2.42.0,<2.43.0

• bioconductor-biostrings >=2.50.0,<2.51.0

• bioconductor-bsgenome >=1.50.0,<1.51.0

• bioconductor-genefilter >=1.64.0,<1.65.0

• bioconductor-iranges >=2.16.0,<2.17.0

• bioconductor-limma >=3.38.0,<3.39.0

• bioconductor-oligo >=1.46.0,<1.47.0

• bioconductor-oligoclasses >=1.44.0,<1.45.0

• bioconductor-preprocesscore >=1.44.0,<1.45.0

• bioconductor-siggenes >=1.56.0,<1.57.0

• bioconductor-sva >=3.30.0,<3.31.0

• r-base >=3.5.1,<3.5.2.0a0

• r-ff

• r-fields

• r-gtools

• r-nor1mix

• r-rcolorbrewer

• r-sqn

Required By

• bioconductor-charmdata

Installation

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

conda install bioconductor-charm

and update with:

conda update bioconductor-charm

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-charm:<tag>

(see bioconductor-charm/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-charm/README.html)