- 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
- 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
- Required By
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¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-qusage/README.html)