recipe bioconductor-annmap

Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/annmap.html

License:

GPL-2

Recipe:

/bioconductor-annmap/meta.yaml

Links:

biotools: annmap, doi: 10.1093/nar/gkm779

annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl. The annmap database can be downloaded from: https://figshare.manchester.ac.uk/account/articles/16685071

package bioconductor-annmap

versions:

1.44.0-0,  1.42.0-0,  1.40.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-1,  1.32.0-0,  1.30.0-0,  1.28.0-0, 

1.44.0-0,  1.42.0-0,  1.40.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-1,  1.32.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-genefilter:

>=1.84.0,<1.85.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dbi:

depends r-digest:

depends r-lattice:

depends r-rmysql:

>=0.6-0

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-annmap

and update with::

   mamba update bioconductor-annmap

To create a new environment, run:

mamba create --name myenvname bioconductor-annmap

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-annmap:<tag>

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

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