recipe bioconductor-r3cpet

3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/R3CPET.html

License:

GPL (>=2)

Recipe:

/bioconductor-r3cpet/meta.yaml

The package provides a method to infer the set of proteins that are more probably to work together to maintain chormatin interaction given a ChIA-PET experiment results.

package bioconductor-r3cpet

versions:

1.32.0-0,  1.30.0-1,  1.30.0-0,  1.26.0-3,  1.26.0-2,  1.26.0-1,  1.24.0-0,  1.22.0-1,  1.22.0-0, 

1.32.0-0,  1.30.0-1,  1.30.0-0,  1.26.0-3,  1.26.0-2,  1.26.0-1,  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-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-ggbio:

>=1.48.0,<1.49.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-clvalid:

depends r-data.table:

depends r-ggplot2:

depends r-hmisc:

depends r-igraph:

depends r-pheatmap:

depends r-rcpp:

>=0.10.4

depends r-rcurl:

depends r-reshape2:

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-r3cpet

and update with::

   mamba update bioconductor-r3cpet

To create a new environment, run:

mamba create --name myenvname bioconductor-r3cpet

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-r3cpet:<tag>

(see `bioconductor-r3cpet/tags`_ for valid values for ``<tag>``)

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