recipe bioconductor-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.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/GenomicFeatures.html

License

Artistic-2.0

Recipe

/bioconductor-genomicfeatures/meta.yaml

Links

biotools: genomicfeatures

package bioconductor-genomicfeatures

(downloads) docker_bioconductor-genomicfeatures

Versions

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

>=1.44.0,<1.45.0

Depends bioconductor-biobase

>=2.42.0,<2.43.0

Depends bioconductor-biocgenerics

>=0.28.0,<0.29.0

Depends bioconductor-biomart

>=2.38.0,<2.39.0

Depends bioconductor-biostrings

>=2.50.0,<2.51.0

Depends bioconductor-genomeinfodb

>=1.18.0,<1.19.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-iranges

>=2.16.0,<2.17.0

Depends bioconductor-rtracklayer

>=1.42.0,<1.43.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends bioconductor-xvector

>=0.22.0,<0.23.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-dbi

Depends r-rcurl

Depends r-rsqlite

>=2.0

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-genomicfeatures

and update with:

conda update bioconductor-genomicfeatures

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-genomicfeatures:<tag>

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

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-genomicfeatures/README.html)