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shinyTANDEM

shinyTANDEM

shinyTANDEM is an R tool to visualize rTANDEM MS/MS protein identification results. shinyTANDEM has GUI functions to construct parameter objects, launch searches, and convert among R objects and XML files.

Topic

Sequencing

Details

  • Operation: Repeat sequence analysis
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v3
  • Cost: Free
  • Version name: 1.26.0
  • Credit: -
  • Contact: frederic.fournier _at_ crchuq.ulaval.ca
  • Collection: Bioconductor

Publications

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


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