DOI: 10.18129/B9.bioc.qusage    

This is the development version of qusage; to use it, please install the devel version of Bioconductor.

qusage: Quantitative Set Analysis for Gene Expression

Bioconductor version: Development (3.10)

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)

Author: Christopher Bolen and Gur Yaari, with contributions from Juilee Thakar, Hailong Meng, Jacob Turner, Derek Blankenship, and Steven Kleinstein

Maintainer: Christopher Bolen <cbolen1 at gmail.com>

Citation (from within R, enter citation("qusage")):


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if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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PDF R Script Running qusage
PDF   Reference Manual


biocViews GeneSetEnrichment, ImmunoOncology, Microarray, RNASeq, Software
Version 2.19.0
In Bioconductor since BioC 2.13 (R-3.0) (5.5 years)
License GPL (>= 2)
Depends R (>= 2.10), limma(>= 3.14), methods
Imports utils, Biobase, nlme, emmeans
URL http://clip.med.yale.edu/qusage
Depends On Me
Imports Me
Suggests Me SigCheck
Links To Me
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Source Package qusage_2.19.0.tar.gz
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Mac OS X 10.11 (El Capitan) qusage_2.19.0.tgz
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