recipe bioconductor-champ

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC






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

(downloads) docker_bioconductor-champ



depends bioconductor-bumphunter:


depends bioconductor-champdata:


depends bioconductor-dmrcate:


depends bioconductor-dnacopy:


depends bioconductor-genomicranges:


depends bioconductor-globaltest:


depends bioconductor-goseq:


depends bioconductor-illumina450probevariants.db:


depends bioconductor-illuminahumanmethylation450kmanifest:


depends bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19:


depends bioconductor-illuminahumanmethylationepicmanifest:


depends bioconductor-illuminaio:


depends bioconductor-impute:


depends bioconductor-limma:


depends bioconductor-marray:


depends bioconductor-minfi:


depends bioconductor-missmethyl:


depends bioconductor-preprocesscore:


depends bioconductor-qvalue:


depends bioconductor-sva:


depends bioconductor-watermelon:


depends r-base:


depends r-combinat:

depends r-dendextend:

depends r-doparallel:

depends r-dt:

depends r-ggplot2:

depends r-hmisc:

depends r-isva:

depends r-kpmt:

depends r-matrixstats:

depends r-plotly:


depends r-plyr:

depends r-prettydoc:

depends r-quadprog:

depends r-rcolorbrewer:

depends r-rmarkdown:

depends r-rpmm:

depends r-shiny:

depends r-shinythemes:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-champ

and update with::

   mamba update bioconductor-champ

To create a new environment, run:

mamba create --name myenvname bioconductor-champ

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-champ/tags`_ for valid values for ``<tag>``)

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