recipe bioconductor-interactionset

Base Classes for Storing Genomic Interaction Data

Homepage:

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

License:

GPL-3.0-only

Recipe:

/bioconductor-interactionset/meta.yaml

Links:

biotools: interactionset

Provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.

package bioconductor-interactionset

versions:

1.34.0-0,  1.30.0-1,  1.30.0-0,  1.28.1-0,  1.26.0-1,  1.26.0-0,  1.22.0-2,  1.22.0-1,  1.22.0-0, 

1.34.0-0,  1.30.0-1,  1.30.0-0,  1.28.1-0,  1.26.0-1,  1.26.0-0,  1.22.0-2,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0a0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0a0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0a0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0a0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0a0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

depends r-matrix:

depends r-rcpp:

requirements:

additional platforms:

linux-aarch64

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-interactionset

and update with::

   mamba update bioconductor-interactionset

To create a new environment, run:

mamba create --name myenvname bioconductor-interactionset

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-interactionset:<tag>

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

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