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logicFS

logicFS

A tool to identify single nucleotide polymorphism (SNP) interactions. The logicFS algorithm uses logic regression among binary variables to identify SNP interactions that can explain the disease status in case-control studies.

Topic

DNA polymorphism; Molecular interactions, pathways and networks

Details

  • Operation: SNP detection
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU LGPL v2
  • Cost: Free
  • Version name: 2.4.0
  • Maturity: Stable
  • Credit: Deutsche Forschungsgemeinschaft
  • Contact: holger.schw _at_ gmx.de
  • Collection: BioConductor

Publications

Schwender H, Ickstadt K "Identification of SNP interactions using logic regression." Biostatistics. 2008 Jan;9(1):187-98. Jun 19. https://doi.org/10.1093/biostatistics/kxm024
PMID: 17578898


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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