- recipe bioconductor-champ
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
- Homepage:
- License:
GPL-3
- Recipe:
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:
2.28.0-0,2.22.0-0,2.20.1-0,2.18.1-1,2.16.0-1,2.14.0-1,2.12.2-0- depends bioconductor-bumphunter:
>=1.40.0,<1.41.0- depends bioconductor-champdata:
>=2.30.0,<2.31.0- depends bioconductor-dmrcate:
>=2.12.0,<2.13.0- depends bioconductor-dnacopy:
>=1.72.0,<1.73.0- depends bioconductor-genomicranges:
>=1.50.0,<1.51.0- depends bioconductor-globaltest:
>=5.52.0,<5.53.0- depends bioconductor-goseq:
>=1.50.0,<1.51.0- depends bioconductor-illumina450probevariants.db:
>=1.34.0,<1.35.0- depends bioconductor-illuminahumanmethylation450kmanifest:
>=0.4.0,<0.5.0- depends bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19:
>=0.6.0,<0.7.0- depends bioconductor-illuminahumanmethylationepicmanifest:
>=0.3.0,<0.4.0- depends bioconductor-illuminaio:
>=0.40.0,<0.41.0- depends bioconductor-impute:
>=1.72.0,<1.73.0- depends bioconductor-limma:
>=3.54.0,<3.55.0- depends bioconductor-marray:
>=1.76.0,<1.77.0- depends bioconductor-minfi:
>=1.44.0,<1.45.0- depends bioconductor-missmethyl:
>=1.32.0,<1.33.0- depends bioconductor-preprocesscore:
>=1.60.0,<1.61.0- depends bioconductor-qvalue:
>=2.30.0,<2.31.0- depends bioconductor-sva:
>=3.46.0,<3.47.0- depends bioconductor-watermelon:
>=2.4.0,<2.5.0- depends r-base:
>=4.2,<4.3.0a0- 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:
>=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
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
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, 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¶
Render an 
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