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>
citation("rTANDEM")):
Installation
To install this package, start R (version "4.0") 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
| Reference Manual |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Proteomics, Software |
| Version | 1.30.0 |
| 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Old Source Packages for BioC 3.12 | Source Archive |