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regioneR

regioneR

regioneR is a tool for the association analysis of genomic regions. The regioneR algorithm uses permutation tests.

Topic

Genomics; GWAS study

Details

  • Operation: Genome comparison; Genome feature comparison
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Artistic-2.0
  • Cost: Free
  • Version name: 1.18.1
  • Maturity: Stable
  • Credit: Spanish Ministry of Economy and Competitiveness, the Carlos III Health Institute, FEDER funds, the Government of Catalonia, the Asociacion Espanola Contra el Cancer (AECC).
  • Contact: Bernat Gel bgel _at_ imppc.org
  • Collection: Bioconductor

Publications

Gel B, Diez-Villanueva A, Serra E, Buschbeck M, Peinado MA, Malinverni R "regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests." Bioinformatics. 2016 Jan 15;32(2):289-91. Epub 2015 Sep 30. https://doi.org/10.1093/bioinformatics/btv562
PMID: 26424858
PMCID: PMC4708104


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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