recipe bioconductor-genomicfeatures

Query the gene models of a given organism/assembly

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/GenomicFeatures.html

License:

Artistic-2.0

Recipe:

/bioconductor-genomicfeatures/meta.yaml

Links:

biotools: genomicfeatures

Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a small collection of TxDb objects in the form of ready-to-install TxDb packages for the most commonly studied organisms. Additionally, the user can easily make a TxDb object (or package) for the organism/assembly of their choice by using the tools from the txdbmaker package.

package bioconductor-genomicfeatures

versions:

1.58.0-0,  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, 

1.58.0-0,  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:

>=1.68.0,<1.69.0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-rtracklayer:

>=1.66.0,<1.67.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-xvector:

>=0.46.0,<0.47.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dbi:

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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