:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-champ' .. highlight: bash bioconductor-champ ================== .. conda:recipe:: bioconductor-champ :replaces_section_title: :noindex: Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC :homepage: https://bioconductor.org/packages/3.17/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. .. conda:package:: bioconductor-champ |downloads_bioconductor-champ| |docker_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: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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 quay.io/biocontainers/bioconductor-champ: (see `bioconductor-champ/tags`_ for valid values for ````) .. |downloads_bioconductor-champ| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-champ.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-champ :alt: (downloads) .. |docker_bioconductor-champ| image:: https://quay.io/repository/biocontainers/bioconductor-champ/status :target: https://quay.io/repository/biocontainers/bioconductor-champ .. _`bioconductor-champ/tags`: https://quay.io/repository/biocontainers/bioconductor-champ?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| 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) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-champ/README.html