rTANDEM, an R/Bioconductor package for MS/MS protein identification.
basic_science · Level V
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- Record sourced from PubMed, PMID 24700319.
- Also identified by DOI 10.1093/bioinformatics/btu178.
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Abstract
rTANDEM is an R/Bioconductor package that interfaces the X!Tandem protein identification algorithm. The package can run the multi-threaded algorithm on proteomic data files directly from R. It also provides functions to convert search parameters and results to/from R as well as functions to manipulate parameters and automate searches. An associated R package, shinyTANDEM, provides a web-based graphical interface to visualize and interpret the results. Together, those two packages form an entry point for a general MS/MS-based proteomic pipeline in R/Bioconductor. rTANDEM and shinyTANDEM are distributed in R/Bioconductor, http://bioconductor.org/packages/release/bioc/. The packages are under open licenses (GPL-3 and Artistice-1.0). frederic.fournier@crchuq.ulaval.ca or arnaud.droit@crchuq.ulaval.ca Supplementary data are available at Bioinformatics online.
Medical subject headings
- Proteomics
- Software
- Tandem Mass Spectrometry
- User-Computer Interface