Package Recipe 'bioconductor-genomicfeatures'

recipe bioconductor-genomicfeatures

Conveniently import and query gene models

Homepage: https://bioconductor.org/packages/3.11/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

1.40.0-0, 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,

1.40.0-0, 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 >=1.50.0,<1.51.0
bioconductor-biobase >=2.48.0,<2.49.0
bioconductor-biocgenerics >=0.34.0,<0.35.0
bioconductor-biomart >=2.44.0,<2.45.0
bioconductor-biostrings >=2.56.0,<2.57.0
bioconductor-genomeinfodb >=1.24.0,<1.25.0
bioconductor-genomicranges >=1.40.0,<1.41.0
bioconductor-iranges >=2.22.0,<2.23.0
bioconductor-rtracklayer >=1.48.0,<1.49.0
bioconductor-s4vectors >=0.26.0,<0.27.0
bioconductor-xvector >=0.28.0,<0.29.0
r-base >=4.0,<4.1.0a0
r-dbi
r-rcurl
r-rsqlite >=2.0

Required By

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 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)