recipe bioconductor-ahpathbankdbs

Metabolites and proteins linked to PathBank pathways (for AnnotationHub)

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-ahpathbankdbs/meta.yaml

The package provides a comprehensive mapping table of metabolites and proteins linked to PathBank pathways. The tables include HMDB, KEGG, ChEBI, CAS, Drugbank, Uniprot IDs. The tables are provided for each of the 10 species ("Homo sapiens", "Escherichia coli", "Mus musculus", "Arabidopsis thaliana", "Saccharomyces cerevisiae", "Bos taurus", "Caenorhabditis elegans", "Rattus norvegicus", "Drosophila melanogaster", and "Pseudomonas aeruginosa"). These table information can be used for Metabolite Set (and other) Enrichment Analysis.

package bioconductor-ahpathbankdbs

(downloads) docker_bioconductor-ahpathbankdbs

versions:

0.99.5-5,  0.99.5-4,  0.99.5-3,  0.99.5-2,  0.99.5-1,  0.99.5-0

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-ahpathbankdbs

and update with::

   mamba update bioconductor-ahpathbankdbs

To create a new environment, run:

mamba create --name myenvname bioconductor-ahpathbankdbs

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-ahpathbankdbs:<tag>

(see `bioconductor-ahpathbankdbs/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-ahpathbankdbs/README.html)