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

(downloads) docker_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>)