rTANDEM

Interfaces the tandem protein identification algorithm in R

Bioconductor version: Development (3.0)

This package interfaces the tandem protein identification algorithm in R. Identification can be launched in the X!Tandem style, by using as sole parameter the path to a parameter file. But rTANDEM aslo provides extended syntax and functions to streamline launching analyses, as well as function to convert results, parameters and taxonomy to/from R. A related package, shinyTANDEM, provides visualization interface for result objects.

Author: Frederic Fournier <frederic.fournier at crchuq.ulaval.ca>, Charles Joly Beauparlant <charles.joly-beauparlant at crchul.ulaval.ca>, Rene Paradis <rene.paradis at genome.ulaval.ca>, Arnaud Droit <arnaud.droit at crchuq.ulaval.ca>

Maintainer: Frederic Fournier <frederic.fournier at crchuq.ulaval.ca>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("rTANDEM")

Documentation

PDF R Script The rTANDEM users guide
PDF   Reference Manual
Text   README
Text   NEWS
Text   LICENSE

Details

biocViews MassSpectrometry, Proteomics, Software
Version 1.5.0
In Bioconductor since BioC 2.12 (R-3.0)
License Artistic-1.0 | file LICENSE
Depends XML, Rcpp, data.table (>= 1.8.8)
Imports methods
Suggests biomaRt
System Requirements rTANDEM uses expat and pthread libraries. See the README file for details.
URL
Depends On Me sapFinder, shinyTANDEM
Imports Me
Suggests Me RforProteomics

Package Downloads

Package Source rTANDEM_1.5.0.tar.gz
Windows Binary rTANDEM_1.5.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) rTANDEM_1.5.0.tgz
Mac OS X 10.9 (Mavericks)
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