PSMatch
This is the development version of PSMatch; for the stable release version, see PSMatch.
Handling and Managing Peptide Spectrum Matches
Bioconductor version: Development (3.21)
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:
Maintainer: Laurent Gatto <laurent.gatto at uclouvain.be>
citation("PSMatch")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | Infrastructure, MassSpectrometry, Proteomics, Software |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 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, omXplore, 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_1.11.0.tar.gz |
| Windows Binary (x86_64) | PSMatch_1.11.0.zip (64-bit only) |
| macOS Binary (x86_64) | PSMatch_1.11.0.tgz |
| macOS Binary (arm64) | PSMatch_1.11.0.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 |