Frédéric Fournier1, Charles Joly Beauparlant1, René Paradis1, Arnaud Droit2. 1. Proteomics Center and Department of Molecular Medicine, CHUQ Research Center, Laval University, Quebec G1V 4G2, Canada. 2. Proteomics Center and Department of Molecular Medicine, CHUQ Research Center, Laval University, Quebec G1V 4G2, CanadaProteomics Center and Department of Molecular Medicine, CHUQ Research Center, Laval University, Quebec G1V 4G2, Canada.
Abstract
SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: 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). CONTACT: frederic.fournier@crchuq.ulaval.ca or arnaud.droit@crchuq.ulaval.ca SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: 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). CONTACT: frederic.fournier@crchuq.ulaval.ca or arnaud.droit@crchuq.ulaval.ca SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.