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.
Gene expression; Microarray experiment; RNA-Seq
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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