synapter

DOI: 10.18129/B9.bioc.synapter    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see synapter.

Label-free data analysis pipeline for optimal identification and quantitation

Bioconductor version: 3.11

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 <lg390 at cam.ac.uk> and Sebastian Gibb <mail at sebastiangibb.de>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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
Text		NEWS

Details

biocViews	ImmunoOncology, MassSpectrometry, Proteomics, QualityControl, Software
Version	2.12.0
In Bioconductor since	BioC 2.11 (R-2.15) (8 years)
License	GPL-2
Depends	R (>= 3.1.0), methods, MSnbase(>= 2.1.2)
Imports	RColorBrewer, lattice, qvalue, multtest, utils, tools, Biobase, knitr, Biostrings, cleaver(>= 1.3.3), readr (>= 0.2), rmarkdown (>= 1.0)
LinkingTo
Suggests	synapterdata(>= 1.13.2), xtable, testthat (>= 0.8), BRAIN, BiocStyle
SystemRequirements
Enhances
URL	https://lgatto.github.io/synapter/
Depends On Me	synapterdata
Imports Me
Suggests Me	pRoloc, RforProteomics
Links To Me
Build Report

Package Archives

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

Source Package	synapter_2.12.0.tar.gz
Windows Binary	synapter_2.12.0.zip
macOS 10.13 (High Sierra)	synapter_2.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/synapter
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/synapter
Package Short Url	https://bioconductor.org/packages/synapter/
Package Downloads Report	Download Stats