To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("synapter")

In most cases, you don't need to download the package archive at all.

synapter

 

Label-free data analysis pipeline for optimal identification and quantitation

Bioconductor version: Release (3.5)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("synapter")

Documentation

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 MassSpectrometry, Proteomics, QualityControl, Software
Version 2.0.0
In Bioconductor since BioC 2.11 (R-2.15) (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
Build Report  

Package Archives

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

Package Source synapter_2.0.0.tar.gz
Windows Binary synapter_2.0.0.zip
Mac OS X 10.11 (El Capitan) synapter_2.0.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/synapter/tree/release-3.5
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: