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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
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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 |
| 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.
| Source Package | 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 |
| Source Repository | git clone https://git.bioconductor.org/packages/synapter |
| Package Short Url | http://bioconductor.org/packages/synapter/ |
| Package Downloads Report | Download Stats |
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