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GWASTools

GWASTools

GWASTools is an R tool for quality control, analysis, and annotation of genome-wide association study (GWAS) data. The package stores data in NetCDF format to allow data sets that exceed the R memory limits.

Topic

GWAS study

Details

  • Operation: Deposition; Analysis; Annotation
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Mac OS X; Microsoft Windows
  • License: Artistic-2.0
  • Cost: Free
  • Version name: 1.32.0
  • Maturity: Stable
  • Credit: National Institutes of Health (NIH), GENEVA Coordinating Center, GARNET Coordinating Center.
  • Contact: Stephanie M. Gogarten sdmorris _at_ uw.edu
  • Collection: Bioconductor

Publications

Gogarten SM, Bhangale T, Conomos MP, Laurie CA, McHugh CP, Painter I, Zheng X, Crosslin DR, Levine D, Lumley T, Nelson SC, Rice K, Shen J, Swarnkar R, Weir BS, Laurie CC "GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies." Bioinformatics 2012; 28(24):3329-31 https://doi.org/10.1093/bioinformatics/bts610
PMID: 23052040
PMCID: PMC3519456


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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