recipe bioconductor-genomicstate

Build and access GenomicState objects for use with derfinder tools from sources like Gencode

Homepage:

https://bioconductor.org/packages/3.17/data/annotation/html/GenomicState.html

License:

Artistic-2.0

Recipe:

/bioconductor-genomicstate/meta.yaml

This package contains functions for building GenomicState objects from different annotation sources such as Gencode. It also provides access to these files at JHPCE.

package bioconductor-genomicstate

versions:

0.99.15-3,  0.99.15-2,  0.99.15-1,  0.99.15-0,  0.99.9-3,  0.99.9-2,  0.99.9-1,  0.99.9-0

depends bioconductor-annotationdbi:

>=1.62.0,<1.63.0

depends bioconductor-annotationhub:

>=3.8.0,<3.9.0

depends bioconductor-bumphunter:

>=1.42.0,<1.43.0

depends bioconductor-data-packages:

>=20230706

depends bioconductor-derfinder:

>=1.34.0,<1.35.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicfeatures:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-org.hs.eg.db:

>=3.17.0,<3.18.0

depends bioconductor-rtracklayer:

>=1.60.0,<1.61.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

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-genomicstate

and update with::

   mamba update bioconductor-genomicstate

To create a new environment, run:

mamba create --name myenvname bioconductor-genomicstate

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-genomicstate:<tag>

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

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