bioconductor-qusage¶
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/3.7/bioc/html/qusage.html |
| Versions | 2.10.0, 2.12.0, 2.14.0 |
| License | GPL (>= 2) |
| Recipe | https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-qusage |
| Links | biotools: 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
A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-qusage.
Link to this page¶
Render an 
badge with the following Markdown:
[](http://bioconda.github.io/recipes/bioconductor-qusage/README.html)
