recipe bioconductor-genestructuretools

Tools for spliced gene structure manipulation and analysis

Homepage:

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

License:

BSD_3_clause + file LICENSE

Recipe:

/bioconductor-genestructuretools/meta.yaml

GeneStructureTools can be used to create in silico alternative splicing events, and analyse potential effects this has on functional gene products.

package bioconductor-genestructuretools

versions:

1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0, 

1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.0-0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-bsgenome.mmusculus.ucsc.mm10:

>=1.4.0,<1.5.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-gviz:

>=1.46.0,<1.47.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-plyr:

depends r-stringdist:

depends r-stringr:

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-genestructuretools

and update with::

   mamba update bioconductor-genestructuretools

To create a new environment, run:

mamba create --name myenvname bioconductor-genestructuretools

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-genestructuretools:<tag>

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

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