recipe bioconductor-genomicfeatures

Conveniently import and query gene models

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-genomicfeatures/meta.yaml

Links:

biotools: genomicfeatures

A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.

package bioconductor-genomicfeatures

versions:

1.54.1-0,  1.52.1-0,  1.50.2-0,  1.46.1-0,  1.44.0-0,  1.42.2-0,  1.42.0-0,  1.40.0-0,  1.38.0-0, 

1.54.1-0,  1.52.1-0,  1.50.2-0,  1.46.1-0,  1.44.0-0,  1.42.2-0,  1.42.0-0,  1.40.0-0,  1.38.0-0,  1.36.4-0,  1.36.0-0,  1.34.1-0,  1.32.3-0,  1.30.3-0,  1.30.0-0,  1.28.5-0,  1.26.4-0,  1.26.0-2,  1.24.5-2,  1.24.5-1,  1.24.5-0,  1.22.13-0,  1.22.6-0,  1.22.4-0,  1.22.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocio:

>=1.12.0,<1.13.0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

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 bioconductor-xvector:

>=0.42.0,<0.43.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dbi:

depends r-rcurl:

depends r-rsqlite:

>=2.0

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-genomicfeatures

and update with::

   mamba update bioconductor-genomicfeatures

To create a new environment, run:

mamba create --name myenvname bioconductor-genomicfeatures

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-genomicfeatures:<tag>

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

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