recipe bioconductor-ensembldb

Utilities to create and use Ensembl-based annotation databases

Homepage:

https://bioconductor.org/packages/3.18/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:

2.26.0-0,  2.24.0-0,  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, 

2.26.0-0,  2.24.0-0,  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:

>=1.64.0,<1.65.0

depends bioconductor-annotationfilter:

>=1.26.0,<1.27.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-protgenerics:

>=1.34.0,<1.35.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-curl:

depends r-dbi:

depends r-rsqlite:

>=1.1

requirements:

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-ensembldb

and update with::

   mamba update bioconductor-ensembldb

To create a new environment, run:

mamba create --name myenvname bioconductor-ensembldb

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-ensembldb:<tag>

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

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