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Bioconductor - synapter

synapter

This package is for version 3.21 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see synapterdata.

Label-free data analysis pipeline for optimal identification and quantitation

Bioconductor version: Release (3.21)

The synapter package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy.

Author: Laurent Gatto, Nick J. Bond, Pavel V. Shliaha and Sebastian Gibb.

Maintainer: Laurent Gatto <laurent.gatto at uclouvain.be> Sebastian Gibb <mail at sebastiangibb.de>

Citation (from within R, enter citation("synapter")): Installation

To install this package, start R (version "4.5") and enter:


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

BiocManager::install("synapter")

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("synapter")
Combining HDMSe/MSe data using 'synapter' to optimise identification and quantitation HTML R Script Fragment matching using 'synapter' HTML R Script Synapter2 and synergise2 HTML R Script Reference Manual PDF Details biocViews ImmunoOncology, MassSpectrometry, Proteomics, QualityControl, Software Version 2.31.0 In Bioconductor since BioC 2.11 (R-2.15) (13 years) License GPL-2 Depends R (>= 3.1.0), methods, MSnbase(>= 2.1.2) Imports RColorBrewer, lattice, qvalue, multtest, utils, tools, Biobase, Biostrings, cleaver(>= 1.3.3), readr (>= 0.2), rmarkdown (>= 1.0) System Requirements URL https://lgatto.github.io/synapter/ See More Package Archives

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

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