rTANDEM is a tool to identify proteins in MS/MS data interfacing the X!Tandem protein identification algorithm. The rTANDEM interface extends the command syntax and has functions to optimize analyses, converts results, parameters, and taxonomy to and from R. The rTANDEM algorithm can run multi-threaded. See associated tools: shinyTANDEM and X!Tandem.
Protein structure analysis
Fournier F, Joly Beauparlant C, Paradis R, Droit A "rTANDEM, an R/Bioconductor package for MS/MS protein identification." Bioinformatics. 2014 Aug 1;30(15):2233-4. Epub 2014 Apr 3. https://doi.org/10.1093/bioinformatics/btu178
PMID: 24700319
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600
If you find errors, please report here.
SECTIONS
TutorialsFind thousands of Bioinformatics and Life Science software tools and databases in the newly launched
Ads