recipe bioconductor-txdbmaker

Tools for making TxDb objects from genomic annotations

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/txdbmaker.html

License:

Artistic-2.0

Recipe:

/bioconductor-txdbmaker/meta.yaml

A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and to import them in a TxDb object. TxDb objects are implemented in the GenomicFeatures package, together with flexible methods for extracting the desired features in convenient formats.

package bioconductor-txdbmaker

versions:

1.2.0-0

depends bioconductor-annotationdbi:

>=1.68.0,<1.69.0

depends bioconductor-biobase:

>=2.66.0,<2.67.0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biocio:

>=1.16.0,<1.17.0

depends bioconductor-biomart:

>=2.62.0,<2.63.0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomicfeatures:

>=1.58.0,<1.59.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-rtracklayer:

>=1.66.0,<1.67.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-ucsc.utils:

>=1.2.0,<1.3.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dbi:

depends r-httr:

depends r-rjson:

depends r-rsqlite:

>=2.0

requirements:

additional platforms:

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-txdbmaker

and update with::

   mamba update bioconductor-txdbmaker

To create a new environment, run:

mamba create --name myenvname bioconductor-txdbmaker

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-txdbmaker:<tag>

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

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