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networkBMA

networkBMA

networkBMA is a tool to infer gene regulatory networks. The networkBMA algorithm uses a Bayesian inference method combining external information to increase accuracy.

Topic

Gene expression; Data visualisation; Bioinformatics; RNA-Seq

Details

  • Operation: RNA-seq time series data analysis; Pathway or network visualisation
  • 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: 2.26.0
  • Maturity: Mature
  • Credit: The National Institutes of Health (NIH), Science Foundation Ireland ETS Walton visitor award.
  • Contact: Ka Yee Yeung kayee _at_ u.washington.edu
  • Collection: Bioconductor

Publications

Young WC, Raftery AE, Yeung KY "Fast Bayesian inference for gene regulatory networks using ScanBMA." BMC Syst Biol 2014 https://doi.org/10.1186/1752-0509-8-47
PMID: 24742092
PMCID: PMC4006459


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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