synapter
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see synapter.
Label-free data analysis pipeline for optimal identification and quantitation
Bioconductor version: 3.9
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("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 | ||
| NEWS | Text |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Proteomics, QualityControl, Software |
| Version | 2.8.0 |
| 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/ |
See More
| 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_2.8.0.tar.gz |
| Windows Binary | synapter_2.8.0.zip |
| Mac OS X 10.11 (El Capitan) | synapter_2.8.0.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 3.9 | Source Archive |