recipe bioconductor-ensembldb

Utilities to create and use Ensembl-based annotation databases

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/ensembldb.html

License:

LGPL

Recipe:

/bioconductor-ensembldb/meta.yaml

Links:

biotools: ensembldb, doi: 10.1038/nmeth.3252

The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.

package bioconductor-ensembldb

Versions:

2.22.0-0,  2.18.1-0,  2.16.0-0,  2.14.0-1,  2.14.0-0,  2.12.1-0,  2.10.0-0,  2.8.0-1,  2.6.3-0, 

2.22.0-0,  2.18.1-0,  2.16.0-0,  2.14.0-1,  2.14.0-0,  2.12.1-0,  2.10.0-0,  2.8.0-1,  2.6.3-0,  2.4.1-0,  2.2.2-0,  2.2.0-0,  2.0.4-0,  1.6.2-0,  1.6.0-0

Depends:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-annotationfilter >=1.22.0,<1.23.0

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-protgenerics >=1.30.0,<1.31.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• r-base >=4.2,<4.3.0a0

• r-curl

• r-dbi

• r-rsqlite >=1.1

Required By:

• bioconductor-ensdb.rnorvegicus.v75

• bioconductor-gviz

• bioconductor-ritan

• bioconductor-signifinder

• bioconductor-consensusde

• bioconductor-chimeraviz

• bioconductor-ensdb.mmusculus.v79

• bioconductor-ensdb.hsapiens.v75

• bioconductor-epivizrdata

• bioconductor-biovizbase

• bioconductor-tximeta

• bioconductor-chippeakanno

• bioconductor-scrnaseq

• bioconductor-singlecelltk

• bioconductor-ensdb.rnorvegicus.v79

• bioconductor-ensdb.hsapiens.v79

• bioconductor-metagene

• bioconductor-genomicdistributionsdata

• bioconductor-ahensdbs

• bioconductor-ggbio

• bioconductor-busparse

• bioconductor-proteasy

• bioconductor-ensdb.mmusculus.v75

• bioconductor-epimutacions

• r-acidgenomes

• bioconductor-drugtargetinteractions

• bioconductor-diffutr

• bioconductor-ensdb.hsapiens.v86

• bioconductor-scanmirapp

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-ensembldb

and update with:

conda update bioconductor-ensembldb

or use the docker container:

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

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

Download stats

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