recipe bioconductor-psmatch

Handling and Managing Peptide Spectrum Matches

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-psmatch/meta.yaml

The PSMatch package helps proteomics practitioners to load, handle and manage Peptide Spectrum Matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions.

package bioconductor-psmatch

versions:

1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-mscoreutils:

>=1.14.0,<1.15.0

depends bioconductor-protgenerics:

>=1.34.0,<1.35.0

depends bioconductor-qfeatures:

>=1.12.0,<1.13.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-igraph:

depends r-matrix:

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-psmatch

and update with::

   mamba update bioconductor-psmatch

To create a new environment, run:

mamba create --name myenvname bioconductor-psmatch

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-psmatch:<tag>

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

Download stats

Link to this page

Render an 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-psmatch/README.html)