recipe bioconductor-pepxmltab

Parsing pepXML files and filter based on peptide FDR.

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-pepxmltab/meta.yaml

Links:

biotools: pepxmltab, doi: 10.1038/nmeth.3252

Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR.

package bioconductor-pepxmltab

(downloads) docker_bioconductor-pepxmltab

versions:
1.36.0-1,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0, 

1.36.0-1,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.1-0,  1.14.0-0,  1.12.0-0,  1.10.0-0

depends r-base:

>=4.3,<4.4.0a0

depends r-xml:

>=3.98-1.1

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-pepxmltab

and update with::

   mamba update bioconductor-pepxmltab

To create a new environment, run:

mamba create --name myenvname bioconductor-pepxmltab

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-pepxmltab:<tag>

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