recipe bioconductor-cohcap

CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/COHCAP.html

License:

GPL-3.0-only

Recipe:

/bioconductor-cohcap/meta.yaml

Links:

biotools: cohcap

COHCAP (pronounced "co-cap") provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k/EPIC methylation array, targeted BS-Seq, etc.). It provides differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, with visualizaton options. Discussion Group: https://sourceforge.net/p/cohcap/discussion/bioconductor/

package bioconductor-cohcap

versions:

1.48.0-1,  1.48.0-0,  1.46.0-0,  1.44.0-1,  1.44.0-0,  1.40.0-3,  1.40.0-2,  1.40.0-1,  1.40.0-0, 

1.48.0-1,  1.48.0-0,  1.46.0-0,  1.44.0-1,  1.44.0-0,  1.40.0-3,  1.40.0-2,  1.40.0-1,  1.40.0-0,  1.38.0-0,  1.36.0-1,  1.36.0-0,  1.34.1-0,  1.32.0-1,  1.30.0-1,  1.30.0-0,  1.28.1-0,  1.26.0-0,  1.24.0-0

depends bioconductor-cohcapanno:

>=1.38.0,<1.39.0

depends bioconductor-cohcapanno:

>=1.38.0,<1.39.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends perl:

>=5.32.1,<5.33.0a0 *_perl5

depends perl:

>=5.6.0

depends r-base:

>=4.3,<4.4.0a0

depends r-bh:

depends r-gplots:

depends r-rcolorbrewer:

depends r-rcpp:

depends r-rcpparmadillo:

depends r-writexls:

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-cohcap

and update with::

   mamba update bioconductor-cohcap

To create a new environment, run:

mamba create --name myenvname bioconductor-cohcap

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-cohcap:<tag>

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

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