DOI: 10.18129/B9.bioc.PSMatch  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see PSMatch.

Handling and Managing Peptide Spectrum Matches

Bioconductor version: 3.17

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.

Author: Laurent Gatto [aut, cre] , Johannes Rainer [aut] , Sebastian Gibb [aut] , Samuel Wieczorek [ctb], Thomas Burger [ctb]

Maintainer: Laurent Gatto <laurent.gatto at>

Citation (from within R, enter citation("PSMatch")):


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HTML R Script MS2 fragment ions
HTML R Script Understanding protein groups with adjacency matrices
HTML R Script Working with PSM data
PDF   Reference Manual
Text   NEWS


biocViews Infrastructure, MassSpectrometry, Proteomics, Software
Version 1.4.0
In Bioconductor since BioC 3.15 (R-4.2) (1.5 years)
License Artistic-2.0
Depends S4Vectors
Imports utils, stats, igraph, methods, Matrix, BiocParallel, BiocGenerics, ProtGenerics(>= 1.27.1), QFeatures, MsCoreUtils
Suggests msdata, rpx, mzID, mzR, Spectra, SummarizedExperiment, BiocStyle, rmarkdown, knitr, factoextra, testthat
Depends On Me
Imports Me
Suggests Me MsDataHub
Links To Me
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