recipe bioconductor-chipenrich

Gene Set Enrichment For ChIP-seq Peak Data

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/chipenrich.html

License:

GPL-3

Recipe:

/bioconductor-chipenrich/meta.yaml

ChIP-Enrich and Poly-Enrich perform gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for confounding factors such as the length of genes, and the mappability of the sequence surrounding genes.

package bioconductor-chipenrich

(downloads) docker_bioconductor-chipenrich

versions:
2.24.0-02.22.0-02.18.0-02.16.0-02.14.0-12.14.0-02.12.0-02.10.0-12.8.0-1

2.24.0-02.22.0-02.18.0-02.16.0-02.14.0-12.14.0-02.12.0-02.10.0-12.8.0-12.6.0-0

depends bioconductor-annotationdbi:

>=1.62.0,<1.63.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-chipenrich.data:

>=2.24.0,<2.25.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-org.dm.eg.db:

>=3.17.0,<3.18.0

depends bioconductor-org.dr.eg.db:

>=3.17.0,<3.18.0

depends bioconductor-org.hs.eg.db:

>=3.17.0,<3.18.0

depends bioconductor-org.mm.eg.db:

>=3.17.0,<3.18.0

depends bioconductor-org.rn.eg.db:

>=3.17.0,<3.18.0

depends bioconductor-rtracklayer:

>=1.60.0,<1.61.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends r-base:

>=4.3,<4.4.0a0

depends r-lattice:

depends r-latticeextra:

depends r-mass:

depends r-mgcv:

depends r-plyr:

depends r-rms:

depends r-stringr:

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-chipenrich

and update with::

   mamba update bioconductor-chipenrich

To create a new environment, run:

mamba create --name myenvname bioconductor-chipenrich

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-chipenrich:<tag>

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

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