synapter

Label-free data analysis pipeline for optimal identification and quantitation

Bioconductor version: Development (3.0)

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 and Pavel V. Shliaha with contributions from Sebastian Gibb.

Maintainer: Laurent Gatto <lg390 at cam.ac.uk>

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("synapter")

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

Documentation

PDF R Script Combining HDMSe/MSe data using 'synapter' to optimise identification and quantitation
PDF   Reference Manual
Text   NEWS

Details

biocViews GUI, MassSpectrometry, Proteomics, Software
Version 1.7.0
In Bioconductor since BioC 2.11 (R-2.15)
License GPL-2
Depends R (>= 2.15), methods, MSnbase
Imports hwriter, tcltk, tcltk2, RColorBrewer, lattice, qvalue, multtest, utils, Biobase, knitr, Biostrings, cleaver, BiocParallel
Suggests synapterdata, xtable
System Requirements
URL http://lgatto.github.com/synapter/
Depends On Me synapterdata
Imports Me
Suggests Me pRoloc, RforProteomics

Package Downloads

Package Source synapter_1.7.0.tar.gz
Windows Binary synapter_1.7.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) synapter_1.7.0.tgz
Mac OS X 10.9 (Mavericks) synapter_1.7.0.tgz
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center