PSMatch

DOI: 10.18129/B9.bioc.PSMatch  

Handling and Managing Peptide Spectrum Matches

Bioconductor version: Release (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 uclouvain.be>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

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

Details

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
LinkingTo
Suggests	msdata, rpx, mzID, mzR, Spectra, SummarizedExperiment, BiocStyle, rmarkdown, knitr, factoextra, testthat
SystemRequirements
Enhances
URL	https://github.com/RforMassSpectrometry/PSM
BugReports	https://github.com/RforMassSpectrometry/PSM/issues
Depends On Me
Imports Me
Suggests Me	MsDataHub
Links To Me
Build Report

Package Archives

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

Source Package	PSMatch_1.4.0.tar.gz
Windows Binary	PSMatch_1.4.0.zip
macOS Binary (x86_64)	PSMatch_1.4.0.tgz
macOS Binary (arm64)	PSMatch_1.4.0.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
Old Source Packages for BioC 3.17	Source Archive