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phosphonormalizer

phosphonormalizer

phosphonormalizer is a tool to normalize mass spectrometry-based label-free phosphoproteomics. The phosphonormalizer algorithm applies the median normalization and uses the overlap between enriched and non-enriched datasets for compensation for the bias caused by global phosphorylation.

Topic

Proteomics; Statistics and probability

Details

  • Operation: Standardisation and normalisation
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU General Public License v>=2
  • Cost: Free
  • Version name: 1.10.0
  • Maturity: Stable
  • Credit: The European Research Council, European Union’s Horizon 2020 research and innovation programme, Academy of Finland, Juvenile Diabetes Research Foundation JDRF, Tekes—the Finnish Funding Agency for Innovation, Sigrid Juselius Foundation.
  • Contact: Sohrab Saraei sohrab.saraei _at_ utu.fi
  • Collection: Bioconductor

Publications

Saraei S, Suomi T, Kauko O, Elo LL, Stegle O "Phosphonormalizer: an R package for normalization of MS-based label-free phosphoproteomics." Bioinformatics 2018; 34(4):693-694 https://doi.org/10.1093/bioinformatics/btx573
PMID: 28968644


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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