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QuSAGE

QuSAGE

QuSAGE (Quantitative Set Analysis of Gene Expression) is a tool quantify and analyze differential gene expression (DGE) and gene to gene correlations in RNA-seq data sets. The QuSAGE algorithm quantifies gene-set activity with a complete probability density function, computes p-values and confidence intervals.

Topic

Gene expression; Microarray experiment; RNA-Seq

Details

  • Operation: Differential gene expression analysis
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GPL-2.0
  • Cost: Free
  • Version name: 2.20.0
  • Maturity: Mature
  • Credit: The National Institute of Allergy and Infectious Diseases contract, the National Institutes of Health.
  • Contact: Christopher Bolen cbolen1 _at_ gmail.com
  • Collection: Bioconductor

Publications

Yaari G, Bolen CR, Thakar J, Kleinstein SH "Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations." Nucleic Acids Res. 2013; 41(18):e170 https://doi.org/10.1093/nar/gkt660
PMID: 23921631
PMCID: PMC3794608


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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