Package Recipe 'bioconductor-champ'

recipe bioconductor-champ¶

The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations.

Homepage: https://bioconductor.org/packages/3.9/bioc/html/ChAMP.html
License: GPL-3
Recipe: /bioconductor-champ/meta.yaml

package bioconductor-champ¶

Versions: 2.12.2-0
Depends bioconductor-bumphunter: >=1.24.0,<1.25.0
Depends bioconductor-champdata: >=2.14.0,<2.15.0
Depends bioconductor-dmrcate: >=1.18.0,<1.19.0
Depends bioconductor-dnacopy: >=1.56.0,<1.57.0
Depends bioconductor-fem: >=3.10.0,<3.11.0
Depends bioconductor-genomicranges: >=1.34.0,<1.35.0
Depends bioconductor-globaltest: >=5.36.0,<5.37.0
Depends bioconductor-goseq: >=1.34.0,<1.35.0
Depends bioconductor-illumina450probevariants.db: >=1.18.0,<1.19.0
Depends bioconductor-illuminahumanmethylation450kmanifest: >=0.4.0,<0.5.0
Depends bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19: >=0.6.0,<0.7.0
Depends bioconductor-illuminahumanmethylationepicmanifest: >=0.3.0,<0.4.0
Depends bioconductor-illuminaio: >=0.24.0,<0.25.0
Depends bioconductor-impute: >=1.56.0,<1.57.0
Depends bioconductor-limma: >=3.38.0,<3.39.0
Depends bioconductor-marray: >=1.60.0,<1.61.0
Depends bioconductor-minfi: >=1.28.0,<1.29.0
Depends bioconductor-missmethyl: >=1.16.0,<1.17.0
Depends bioconductor-preprocesscore: >=1.44.0,<1.45.0
Depends bioconductor-qvalue: >=2.14.0,<2.15.0
Depends bioconductor-sva: >=3.30.0,<3.31.0
Depends bioconductor-watermelon: >=1.26.0,<1.27.0
Depends r-base: >=3.5.1,<3.5.2.0a0
Depends r-combinat
Depends r-dendextend
Depends r-doparallel
Depends r-hmisc
Depends r-isva
Depends r-kpmt
Depends r-matrixstats
Depends r-plotly: >=4.5.6
Depends r-plyr
Depends r-prettydoc
Depends r-quadprog
Depends r-rcolorbrewer
Depends r-rmarkdown
Depends r-rpmm
Depends r-shiny
Depends r-shinythemes
Requirements

Installation

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

conda install bioconductor-champ

and update with:

conda update bioconductor-champ

or use the docker container:

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

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