PSMatch

DOI: 10.18129/B9.bioc.PSMatch    

Handling and Managing Peptide Spectrum Matches

Bioconductor version: Release (3.15)

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 "4.2") 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 1.0.0
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
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
Links To Me
Build Report  

Package Archives

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

Source Package PSMatch_1.0.0.tar.gz
Windows Binary PSMatch_1.0.0.zip (64-bit only)
macOS 10.13 (High Sierra) PSMatch_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/PSMatch
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PSMatch
Package Short Url https://bioconductor.org/packages/PSMatch/
Package Downloads Report Download Stats

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