recipe bioconductor-uniprot.ws

R Interface to UniProt Web Services

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/UniProt.ws.html

License:

Artistic-2.0

Recipe:

/bioconductor-uniprot.ws/meta.yaml

Links:

biotools: uniprot.ws, doi: 10.1038/nmeth.3252

The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. This package provides a collection of functions for retrieving, processing, and re-packaging UniProt web services. The package makes use of UniProt's modernized REST API and allows mapping of identifiers accross different databases.

package bioconductor-uniprot.ws

versions:

2.42.0-0,  2.40.1-0,  2.38.0-0,  2.34.0-0,  2.32.0-0,  2.30.0-1,  2.30.0-0,  2.29.0-0,  2.28.0-0, 

2.42.0-0,  2.40.1-0,  2.38.0-0,  2.34.0-0,  2.32.0-0,  2.30.0-1,  2.30.0-0,  2.29.0-0,  2.28.0-0,  2.26.0-0,  2.24.1-0,  2.22.0-0,  2.20.4-0,  2.18.0-0,  2.16.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-biocbaseutils:

>=1.4.0,<1.5.0

depends bioconductor-biocfilecache:

>=2.10.0,<2.11.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends r-base:

>=4.3,<4.4.0a0

depends r-httpcache:

depends r-httr:

depends r-jsonlite:

depends r-progress:

depends r-rjsoncons:

depends r-rsqlite:

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-uniprot.ws

and update with::

   mamba update bioconductor-uniprot.ws

To create a new environment, run:

mamba create --name myenvname bioconductor-uniprot.ws

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-uniprot.ws:<tag>

(see `bioconductor-uniprot.ws/tags`_ for valid values for ``<tag>``)

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