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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("rTANDEM")
In most cases, you don't need to download the package archive at all.
rTANDEM
Interfaces the tandem protein identification algorithm in R
Bioconductor version: 3.0
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 and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("rTANDEM")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rTANDEM")
| R Script | The rTANDEM users guide | |
| Reference Manual | ||
| Text | README | |
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | MassSpectrometry, Proteomics, Software |
| Version | 1.6.1 |
| In Bioconductor since | BioC 2.12 (R-3.0) |
| 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 | sapFinder, shinyTANDEM |
| Imports Me | proteoQC |
| Suggests Me | RforProteomics |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | rTANDEM_1.6.1.tar.gz |
| Windows Binary | rTANDEM_1.6.1.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | rTANDEM_1.6.1.tgz |
| Mac OS X 10.9 (Mavericks) | rTANDEM_1.6.1.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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