PSMatch

This is the released version of PSMatch; for the devel version, see PSMatch.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15

Handling and Managing Peptide Spectrum Matches

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-1520-2268 , Johannes Rainer [aut] ORCID: 0000-0002-6977-7147 , Sebastian Gibb [aut] ORCID: 0000-0001-7406-4443 , Samuel Wieczorek [ctb], Thomas Burger [ctb], Guillaume Deflandre [ctb] ORCID: 0009-0008-1257-2416

Maintainer: Laurent Gatto <laurent.gatto at uclouvain.be>

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

Laurent Gatto, Johannes Rainer, Sebastian Gibb. PSMatch: Handling and Managing Peptide Spectrum Matches. doi:10.18129/B9.bioc.PSMatch, R package version 1.16.0, https://bioconductor.org/packages/PSMatch.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Infrastructure, MassSpectrometry, Proteomics, Software
Version	1.16.0
In Bioconductor since	BioC 3.15 (R-4.2) (4.5 years)
License	Artistic-2.0
Depends	S4Vectors, R (>= 4.1.0), PTMods (>= 0.99.4)
Imports	utils, stats, igraph, methods, Spectra (>= 1.17.10), 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

Suggests	MsDataHub, rpx, mzID, mzR, SummarizedExperiment, BiocStyle, rmarkdown, knitr, factoextra, vdiffr (>= 1.0.0), testthat
Linking To
Enhances
Depends On Me
Imports Me	MSnbase, omXplore, topdownr
Suggests Me	MsDataHub
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	PSMatch_1.16.0.tar.gz
Windows Binary (x86_64)	PSMatch_1.16.0.zip
macOS Binary (big-sur-x86_64)	PSMatch_1.16.0.tgz
macOS Binary (sonoma-arm64)	PSMatch_1.16.0.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