recipe bioconductor-msnid

Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. Also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/MSnID.html

License

Artistic-2.0

Recipe

/bioconductor-msnid/meta.yaml

Links

biotools: msnid, doi: 10.1038/nmeth.3252

package bioconductor-msnid

(downloads) docker_bioconductor-msnid

Versions

1.16.1-0, 1.12.1-0

Depends bioconductor-biobase

>=2.42.0,<2.43.0

Depends bioconductor-msnbase

>=2.8.0,<2.9.0

Depends bioconductor-mzid

>=1.20.0,<1.21.0

Depends bioconductor-mzr

>=2.16.0,<2.17.0

Depends bioconductor-protgenerics

>=1.14.0,<1.15.0

Depends libgcc-ng

>=7.3.0

Depends libstdcxx-ng

>=7.3.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-data.table

Depends r-doparallel

Depends r-dplyr

Depends r-foreach

Depends r-iterators

Depends r-r.cache

Depends r-rcpp

Depends r-reshape2

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-msnid

and update with:

conda update bioconductor-msnid

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-msnid:<tag>

(see bioconductor-msnid/tags for valid values for <tag>)