synapter

DOI: 10.18129/B9.bioc.synapter  

Label-free data analysis pipeline for optimal identification and quantitation

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Combining HDMSe/MSe data using 'synapter' to optimise identification and quantitation
HTML	R Script	Fragment matching using 'synapter'
HTML	R Script	Synapter2 and synergise2
PDF		Reference Manual

Details

biocViews	ImmunoOncology, MassSpectrometry, Proteomics, QualityControl, Software
Version	2.22.0
In Bioconductor since	BioC 2.11 (R-2.15) (10.5 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)
LinkingTo
Suggests	synapterdata(>= 1.13.2), xtable, testthat (>= 0.8), BRAIN, BiocStyle, knitr
SystemRequirements
Enhances
URL	https://lgatto.github.io/synapter/
Depends On Me	synapterdata
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	synapter_2.22.0.tar.gz
Windows Binary	synapter_2.22.0.zip
macOS Binary (x86_64)	synapter_2.22.0.tgz
macOS Binary (arm64)	synapter_2.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/synapter
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/synapter
Bioc Package Browser	https://code.bioconductor.org/browse/synapter/
Package Short Url	https://bioconductor.org/packages/synapter/
Package Downloads Report	Download Stats