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("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 | R Script | |
| Reference Manual | ||
| 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 |