rTANDEM

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see rTANDEM.

Interfaces the tandem protein identification algorithm in R


Bioconductor version: 3.9

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>

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

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rTANDEM")

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

Details

biocViews ImmunoOncology, MassSpectrometry, Proteomics, Software
Version 1.24.0
In Bioconductor since BioC 2.12 (R-3.0) (11 years)
License Artistic-1.0 | file LICENSE
Depends XML, Rcpp, data.table (>= 1.8.8)
Imports methods
System Requirements rTANDEM uses expat and pthread libraries. See the README file for details.
URL
See More
Suggests biomaRt
Linking To Rcpp
Enhances
Depends On Me PGA, sapFinder, shinyTANDEM
Imports Me proteoQC
Suggests Me RforProteomics
Links To Me
Build Report Build Report

Package Archives

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

Source Package rTANDEM_1.24.0.tar.gz
Windows Binary rTANDEM_1.24.0.zip
Mac OS X 10.11 (El Capitan) rTANDEM_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/rTANDEM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rTANDEM
Bioc Package Browser https://code.bioconductor.org/browse/rTANDEM/
Package Short Url https://bioconductor.org/packages/rTANDEM/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive