synapter

DOI: 10.18129/B9.bioc.synapter    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see synapter.

Label-free data analysis pipeline for optimal identification and quantitation

Bioconductor version: 3.8

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>

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

Installation

To install this package, start R (version "3.5") 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 2.6.1
In Bioconductor since BioC 2.11 (R-2.15) (6.5 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_2.6.1.tar.gz
Windows Binary synapter_2.6.1.zip
Mac OS X 10.11 (El Capitan) synapter_2.6.1.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 http://bioconductor.org/packages/synapter/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: