bioconductor-qusage

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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)

Home http://bioconductor.org/packages/3.6/bioc/html/qusage.html
Versions 2.10.0, 2.12.0
License GPL (>= 2)
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-qusage

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-qusage

and update with:

conda update bioconductor-qusage

docker

A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-qusage.