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DEXUS

DEXUS

DEXUS is a tool for the analysis of differential gene expression (DGE) in RNA-seq data where the conditions are unknown. The DEXUS algorithm uses a finite mixture of the negative binomial distribution to model read counts.

Topic

RNA-Seq; Gene expression

Details

  • Operation: Differential gene expression analysis
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU General Public License v>=2
  • Cost: Free
  • Version name: 1.26.0
  • Maturity: Mature
  • Credit: Institute of Bioinformatics, Johannes Kepler University Linz.
  • Contact: Guenter Klambauer klambauer _at_ bioinf.jku.at
  • Collection: Bioconductor

Publications

Klambauer G, Unterthiner T, Hochreiter S "DEXUS: identifying differential expression in RNA-Seq studies with unknown conditions." Nucleic Acids Res. 2013; 41(21):e198 https://doi.org/10.1093/nar/gkt834
PMID: 24049071
PMCID: PMC3834838


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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