Package: qusage
Version: 1.2.0
Date: 2013-01-20
Title: qusage: Quantitative Set Analysis for Gene Expression
Authors@R: c(person("Christopher Bolen", "Developer", role = c("aut",
        "cre"), email = "cbolen1@gmail.com"), person("Gur Yaari",
        "Developer", role = "aut"), person("Juilee Thakar",
        "Developer", role = "aut"), person("Steven Kleinstein",
        "Developer", role = "aut"))
Author: Christopher Bolen and Gur Yaari, with contributions from Juilee Thakar and Steven Kleinstein
Maintainer: Christopher Bolen <cbolen1@gmail.com>
Depends: R (>= 2.10), limma (>= 3.14), methods
Imports: utils, Biobase
Description: This package is an implementation the Quantitative Set Analysis for Gene Expression (QuSAGE) method described in (Yaari G. et al, Nucl Acids Res, 2013). This is a novel Gene Set Enrichment-type test, which is designed to provide a faster, more accurate, and easier to understand test for gene expression studies. qusage accounts for inter-gene correlations using the Variance Inflation Factor technique proposed by Wu et al. (Nucleic Acids Res, 2012). In addition, rather than simply evaluating the deviation from a null hypothesis with a single number (a P value), qusage quantifies gene set activity with a complete probability density function (PDF). From this PDF, P values and confidence intervals can be easily extracted. Preserving the PDF also allows for post-hoc analysis (e.g., pair-wise comparisons of gene set activity) while maintaining statistical traceability. Finally, while qusage is compatible with individual gene statistics from existing methods (e.g., LIMMA), a Welch-based method is implemented that is shown to improve specificity. For questions, contact Chris Bolen (cbolen1@gmail.com) or Steven Kleinstein (steven.kleinstein@yale.edu)
biocViews: Enrichment, GeneSetEnrichment, Bioinformatics, Microarrays,
        RNAseq, Software
License: GPL (>= 2)
URL: http://clip.med.yale.edu/qusage
Packaged: 2013-10-15 08:27:17 UTC; biocbuild
Built: R 3.0.2; ; 2013-10-15 15:48:09 UTC; windows
