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PSMatch

This is the development version of PSMatch; for the stable release version, see PSMatch.

Handling and Managing Peptide Spectrum Matches


Bioconductor version: Development (3.19)

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 uclouvain.be>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("PSMatch")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

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

Details

biocViews Infrastructure, MassSpectrometry, Proteomics, Software
Version 1.7.2
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License Artistic-2.0
Depends S4Vectors
Imports utils, stats, igraph, methods, Matrix, BiocParallel, BiocGenerics, ProtGenerics(>= 1.27.1), QFeatures, MsCoreUtils
System Requirements
URL https://github.com/RforMassSpectrometry/PSM
Bug Reports https://github.com/RforMassSpectrometry/PSM/issues
See More
Suggests msdata, rpx, mzID, mzR, Spectra, SummarizedExperiment, BiocStyle, rmarkdown, knitr, factoextra, testthat
Linking To
Enhances
Depends On Me
Imports Me MSnbase, topdownr
Suggests Me MsDataHub
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package PSMatch_1.7.2.tar.gz
Windows Binary PSMatch_1.7.2.zip
macOS Binary (x86_64) PSMatch_1.7.2.tgz
macOS Binary (arm64) PSMatch_1.7.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/PSMatch
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PSMatch
Bioc Package Browser https://code.bioconductor.org/browse/PSMatch/
Package Short Url https://bioconductor.org/packages/PSMatch/
Package Downloads Report Download Stats