rTANDEM

DOI: 10.18129/B9.bioc.rTANDEM    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.12 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: 3.12

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 "4.0") 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

PDF		Reference Manual

Details

biocViews	ImmunoOncology, MassSpectrometry, Proteomics, Software
Version	1.30.0
In Bioconductor since	BioC 2.12 (R-3.0) (8 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
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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	https://bioconductor.org/packages/rTANDEM/
Package Downloads Report	Download Stats