bioconda / packages / bioconductor-qusage 2.28.0

qusage: Quantitative Set Analysis for Gene Expression


Info: This package contains files in non-standard labels.

conda install

  • linux-64  v2.14.0
  • osx-64  v2.14.0
  • noarch  v2.28.0
To install this package with conda run one of the following:
conda install -c bioconda bioconductor-qusage
conda install -c bioconda/label/gcc7 bioconductor-qusage
conda install -c bioconda/label/cf201901 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. The QuSAGE package also includes a mixed effects model implementation, as described in (Turner JA et al, BMC Bioinformatics, 2015), and a meta-analysis framework as described in (Meng H, et al. PLoS Comput Biol. 2019). For questions, contact Chris Bolen ([email protected]) or Steven Kleinstein ([email protected])

© 2022 Anaconda, Inc. All Rights Reserved. (v2.36.1 bb641a2e) Legal | Privacy Policy