recipe bioconductor-comet

coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns

Homepage:

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

License:

GPL (>= 2)

Recipe:

/bioconductor-comet/meta.yaml

Visualisation of EWAS results in a genomic region. In addition to phenotype-association P-values, coMET also generates plots of co-methylation patterns and provides a series of annotation tracks. It can be used to other omic-wide association scans as lon:g as the data can be translated to genomic level and for any species.

package bioconductor-comet

versions:

1.32.0-0,  1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1, 

1.32.0-0,  1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.14.0-0

depends bioconductor-biomart:

>=2.56.0,<2.57.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-gviz:

>=1.44.0,<1.45.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

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-corrplot:

depends r-gridextra:

depends r-hash:

depends r-psych:

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-comet

and update with::

   mamba update bioconductor-comet

To create a new environment, run:

mamba create --name myenvname bioconductor-comet

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-comet:<tag>

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

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