recipe bioconductor-ahwikipathwaysdbs

Metabolites linked to WikiPathways pathways (for AnnotationHub)

Homepage:

https://bioconductor.org/packages/3.18/data/annotation/html/AHWikipathwaysDbs.html

License:

Artistic-2.0

Recipe:

/bioconductor-ahwikipathwaysdbs/meta.yaml

The package provides a comprehensive mapping table of metabolites linked to Wikipathways pathways. The tables include HMDB, KEGG, ChEBI, Drugbank, PubChem compound, ChemSpider, KNApSAcK, and Wikidata IDs plus CAS and InChIKey. The tables are provided for each of the 25 species ("Anopheles gambiae", "Arabidopsis thaliana", "Bacillus subtilis", "Bos taurus", "Caenorhabditis elegans", "Canis familiaris", "Danio rerio", "Drosophila melanogaster", "Equus caballus", "Escherichia coli", "Gallus gallus", "Gibberella zeae", "Homo sapiens", "Hordeum vulgare", "Mus musculus", "Mycobacterium tuberculosis", "Oryza sativa", "Pan troglodytes", "Plasmodium falciparum", "Populus trichocarpa", "Rattus norvegicus", "Saccharomyces cerevisiae", "Solanum lycopersicum", "Sus scrofa", "Zea mays"). These table information can be used for Metabolite Set Enrichment Analysis.

package bioconductor-ahwikipathwaysdbs

(downloads) docker_bioconductor-ahwikipathwaysdbs

versions:

0.99.4-5,  0.99.4-4,  0.99.4-3,  0.99.4-2,  0.99.4-1,  0.99.4-0

depends bioconductor-annotationhub:

>=3.10.0,<3.11.0

depends bioconductor-data-packages:

>=20231203

depends curl:

depends r-base:

>=4.3,<4.4.0a0

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-ahwikipathwaysdbs

and update with::

   mamba update bioconductor-ahwikipathwaysdbs

To create a new environment, run:

mamba create --name myenvname bioconductor-ahwikipathwaysdbs

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-ahwikipathwaysdbs:<tag>

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

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Link to this page

Render an install-with-bioconda 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-ahwikipathwaysdbs/README.html)