BIOCONDUCTOR . ORG {
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Title:
Bioconductor - qusage
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. 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])
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Keywords {๐}
package, bioconductor, qusage, gene, set, packages, version, analysis, expression, bolen, quantitative, pdf, release, yaari, kleinstein, source, method, acids, res, turner, meng, enter, install, binary, learn, developers, started, software, implementation, test, correlations, nucleic, activity, methods, limma, bmc, bioinformatics, metaanalysis, plos, biol, contact, steven, christopher, thakar, blankenship, installation, start, documentation, system, details,
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org/packages/qusage source repository joint galaxy/bioconductor conference ๏ฟฝgene set meta-analysis bioconductor release tgz source repository inter-gene correlations source package gene set activity quantitative set analysis ๏ฟฝquantitative set analysis gene expression studies individual gene statistics release //code meta-analysis framework bioconductor support site post-hoc analysis nucl acids res nucleic acids res pair-wise comparisons maintaining statistical traceability plos comput biol script reference manual gz windows binary zip macos binary tgz macos binary qusage package git clone https contact chris bolen package installed details biocviews fftw system requirements gene expression welch-based method packages started install package understand test software version bioconductor //bioconductor qusage accounts running qusage christopher bolen org registration open simply evaluating null hypothesis single number confidence intervals
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