rTANDEM

DOI: 10.18129/B9.bioc.rTANDEM    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see rTANDEM.

Interfaces the tandem protein identification algorithm in R

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	ImmunoOncology, MassSpectrometry, Proteomics, Software
Version	1.22.1
In Bioconductor since	BioC 2.12 (R-3.0) (6 years)
License	Artistic-1.0 | file LICENSE
Depends	XML, Rcpp, data.table (>= 1.8.8)
Imports	methods
LinkingTo	Rcpp
Suggests	biomaRt
SystemRequirements	rTANDEM uses expat and pthread libraries. See the README file for details.
Enhances
URL
Depends On Me	PGA, sapFinder, shinyTANDEM
Imports Me	proteoQC
Suggests Me	RforProteomics
Links To Me
Build Report

Package Archives

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

Source Package	rTANDEM_1.22.1.tar.gz
Windows Binary	rTANDEM_1.22.1.zip
Mac OS X 10.11 (El Capitan)	rTANDEM_1.22.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/rTANDEM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/rTANDEM
Package Short Url	http://bioconductor.org/packages/rTANDEM/
Package Downloads Report	Download Stats