recipe bioconductor-genomicranges

Representation and manipulation of genomic intervals

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-genomicranges/meta.yaml

Links:

biotools: genomicranges

The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.

package bioconductor-genomicranges

versions:

1.52.0-0,  1.50.0-1,  1.50.0-0,  1.46.1-1,  1.46.1-0,  1.46.0-0,  1.44.0-0,  1.42.0-1,  1.42.0-0, 

1.52.0-0,  1.50.0-1,  1.50.0-0,  1.46.1-1,  1.46.1-0,  1.46.0-0,  1.44.0-0,  1.42.0-1,  1.42.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-1,  1.34.0-0,  1.32.7-0,  1.30.3-0,  1.30.0-0,  1.28.6-0,  1.26.4-0,  1.26.1-1,  1.24.3-1,  1.22.4-0,  1.22.3-0,  1.22.2-0,  1.22.1-0,  1.22.0-0,  1.20.8-0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-xvector:

>=0.40.0,<0.41.0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

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-genomicranges

and update with::

   mamba update bioconductor-genomicranges

To create a new environment, run:

mamba create --name myenvname bioconductor-genomicranges

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-genomicranges:<tag>

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

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