recipe bioconductor-cexor

An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

Homepage:

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

License:

Artistic-2.0 | GPL-2 + file LICENSE

Recipe:

/bioconductor-cexor/meta.yaml

Links:

biotools: cexor, doi: 10.14806/ej.21.0.837

Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Then, irreproducible discovery rate for overlapping peak-pairs across biological replicates is computed.

package bioconductor-cexor

versions:

1.40.0-0,  1.38.0-0,  1.36.0-0,  1.32.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1, 

1.40.0-0,  1.38.0-0,  1.36.0-0,  1.32.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.8.0-0

depends bioconductor-genomation:

>=1.34.0,<1.35.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-idr:

depends r-rcolorbrewer:

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-cexor

and update with::

   mamba update bioconductor-cexor

To create a new environment, run:

mamba create --name myenvname bioconductor-cexor

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-cexor:<tag>

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

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