recipe bioconductor-msnid

Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/MSnID.html

License:

Artistic-2.0

Recipe:

/bioconductor-msnid/meta.yaml

Links:

biotools: msnid, doi: 10.1038/nmeth.3252

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.

package bioconductor-msnid

Versions:

1.32.0-0,  1.28.0-2,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0, 

1.32.0-0,  1.28.0-2,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.1-0,  1.16.1-0,  1.12.1-0

Depends:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-annotationhub >=3.6.0,<3.7.0

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biocstyle >=2.26.0,<2.27.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-msmstests >=1.36.0,<1.37.0

• bioconductor-msnbase >=2.24.0,<2.25.0

• bioconductor-mzid >=1.36.0,<1.37.0

• bioconductor-mzr >=2.32.0,<2.33.0

• bioconductor-protgenerics >=1.30.0,<1.31.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

• r-data.table

• r-doparallel

• r-dplyr

• r-foreach

• r-ggplot2

• r-iterators

• r-purrr

• r-r.cache

• r-rcpp

• r-reshape2

• r-rlang

• r-runit

• r-stringr

• r-tibble

• r-xtable

Required By:

Installation

With an activated Bioconda channel (see 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>)

Download stats

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