recipe bioconductor-champ

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Homepage

https://bioconductor.org/packages/3.14/bioc/html/ChAMP.html

License

GPL-3

Recipe

/bioconductor-champ/meta.yaml

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.

package bioconductor-champ

Versions

2.22.0-0,  2.20.1-0,  2.18.1-1,  2.16.0-1,  2.14.0-1,  2.12.2-0

Depends

• bioconductor-bumphunter >=1.34.0,<1.35.0

• bioconductor-champdata >=2.24.0,<2.25.0

• bioconductor-dmrcate >=2.6.0,<2.7.0

• bioconductor-dnacopy >=1.66.0,<1.67.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-globaltest >=5.46.0,<5.47.0

• bioconductor-goseq >=1.44.0,<1.45.0

• bioconductor-illumina450probevariants.db >=1.28.0,<1.29.0

• bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0

• bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0

• bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0

• bioconductor-illuminaio >=0.34.0,<0.35.0

• bioconductor-impute >=1.66.0,<1.67.0

• bioconductor-limma >=3.48.0,<3.49.0

• bioconductor-marray >=1.70.0,<1.71.0

• bioconductor-minfi >=1.38.0,<1.39.0

• bioconductor-missmethyl >=1.26.0,<1.27.0

• bioconductor-preprocesscore >=1.54.0,<1.55.0

• bioconductor-qvalue >=2.24.0,<2.25.0

• bioconductor-sva >=3.40.0,<3.41.0

• bioconductor-watermelon >=1.36.0,<1.37.0

• r-base >=4.1,<4.2.0a0

• r-combinat

• r-dendextend

• r-doparallel

• r-dt

• r-ggplot2

• r-hmisc

• r-isva

• r-kpmt

• r-matrixstats

• r-plotly >=4.5.6

• r-plyr

• r-prettydoc

• r-quadprog

• r-rcolorbrewer

• r-rmarkdown

• r-rpmm

• r-shiny

• r-shinythemes

Required By

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>)

Download stats

Link to this page

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