synapter

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see synapter.

Label-free data analysis pipeline for optimal identification and quantitation

Bioconductor version: 3.10

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 "3.6") 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")

Combining HDMSe/MSe data using 'synapter' to optimise identification and quantitation HTML R Script

Fragment matching using 'synapter' HTML R Script

Synapter2 and synergise2 HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ImmunoOncology, MassSpectrometry, Proteomics, QualityControl, Software

Version 2.10.0

In Bioconductor since BioC 2.11 (R-2.15) (11.5 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)

System Requirements

URL https://lgatto.github.io/synapter/

Suggests synapterdata(>= 1.13.2), xtable, testthat (>= 0.8), BRAIN, BiocStyle

Linking To

Enhances

Depends On Me synapterdata

Imports Me

Suggests Me pRoloc, RforProteomics

Links To Me

Build Report Build Report

Package Archives

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

Source Package synapter_2.10.0.tar.gz

Windows Binary synapter_2.10.0.zip

Mac OS X 10.11 (El Capitan) synapter_2.10.0.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

Old Source Packages for BioC 3.10 Source Archive