recipe bioconductor-qusage

qusage: Quantitative Set Analysis for Gene Expression

Homepage

https://bioconductor.org/packages/3.14/bioc/html/qusage.html

License

GPL (>= 2)

Recipe

/bioconductor-qusage/meta.yaml

Links

biotools: 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 (cbolen1@gmail.com) or Steven Kleinstein (steven.kleinstein@yale.edu)

package bioconductor-qusage

Versions

2.28.0-0,  2.26.0-0,  2.24.0-1,  2.24.0-0,  2.22.0-0,  2.20.0-0,  2.18.0-1,  2.16.1-0,  2.16.0-0, 

2.28.0-0,  2.26.0-0,  2.24.0-1,  2.24.0-0,  2.22.0-0,  2.20.0-0,  2.18.0-1,  2.16.1-0,  2.16.0-0,  2.14.0-0,  2.12.0-0,  2.10.0-0

Depends

• bioconductor-biobase >=2.54.0,<2.55.0

• bioconductor-limma >=3.50.0,<3.51.0

• r-base >=4.1,<4.2.0a0

• r-emmeans

• r-fftw

• r-nlme

Required By

• r-beyondcell

Installation

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

conda install bioconductor-qusage

and update with:

conda update bioconductor-qusage

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-qusage:<tag>

(see bioconductor-qusage/tags for valid values for <tag>)

Download stats

Link to this page

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