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.







biotools: genomicfeatures

package bioconductor-genomicfeatures

(downloads) docker_bioconductor-genomicfeatures


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


Depends bioconductor-biobase


Depends bioconductor-biocgenerics


Depends bioconductor-biomart


Depends bioconductor-biostrings


Depends bioconductor-genomeinfodb


Depends bioconductor-genomicranges


Depends bioconductor-iranges


Depends bioconductor-rtracklayer


Depends bioconductor-s4vectors


Depends bioconductor-xvector


Depends r-base


Depends r-dbi

Depends r-rcurl

Depends r-rsqlite




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<tag>

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