rTANDEM, an R/Bioconductor package for MS/MS protein identification.

Conclusions: 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. Methods: 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).

Background: frederic.fournier@crchuq.ulaval.ca or arnaud.droit@crchuq.ulaval.ca Background: Supplementary data are available at Bioinformatics online.