recipe bioconductor-genomicinteractionnodes

A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data

Homepage:

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

License:

file LICENSE

Recipe:

/bioconductor-genomicinteractionnodes/meta.yaml

The GenomicInteractionNodes package can import interactions from bedpe file and define the interaction nodes, the genomic interaction sites with multiple interaction loops. The interaction nodes is a binding platform regulates one or multiple genes. The detected interaction nodes will be annotated for downstream validation.

package bioconductor-genomicinteractionnodes

versions:

1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-go.db:

>=3.18.0,<3.19.0

depends bioconductor-graph:

>=1.80.0,<1.81.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rbgl:

>=1.78.0,<1.79.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

requirements:

additional platforms:

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-genomicinteractionnodes

and update with::

   mamba update bioconductor-genomicinteractionnodes

To create a new environment, run:

mamba create --name myenvname bioconductor-genomicinteractionnodes

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-genomicinteractionnodes:<tag>

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

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