Package Recipe 'bioconductor-ensembldb'

recipe bioconductor-ensembldb

Utilities to create and use Ensembl-based annotation databases

Homepage:: https://bioconductor.org/packages/3.20/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:

2.34.0-0, 2.30.0-0, 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,

2.34.0-0, 2.30.0-0, 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:

on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-annotationfilter >=1.34.0,<1.35.0
on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-genomeinfodb >=1.46.0,<1.47.0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-protgenerics >=1.42.0,<1.43.0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on r-base >=4.5,<4.6.0a0
on r-curl
on r-dbi
on r-rsqlite >=1.1

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-ensembldb

to add into an existing workspace instead, run:

pixi add bioconductor-ensembldb

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-ensembldb

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-ensembldb

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

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-ensembldb/README.html)