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Showing content from http://bioconductor.org/packages/devel/bioc/html/../../bioc/html/../../bioc/html/PSMatch.html below:

Bioconductor - PSMatch (development version)

PSMatch

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

Handling and Managing Peptide Spectrum Matches

Bioconductor version: Development (3.22)

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")): 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")
Details biocViews Infrastructure, MassSpectrometry, Proteomics, Software Version 1.13.1 In Bioconductor since BioC 3.15 (R-4.2) (3 years) License Artistic-2.0 Depends S4Vectors, R (>= 4.1.0) Imports utils, stats, igraph, methods, Spectra(>= 1.17.10), Matrix, BiocParallel, BiocGenerics, ProtGenerics(>= 1.27.1), QFeatures, MsCoreUtils, IRanges System Requirements URL https://github.com/RforMassSpectrometry/PSM Bug Reports https://github.com/RforMassSpectrometry/PSM/issues See More Suggests msdata, 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 Package Archives

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

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