recipe bioconductor-qusage

qusage: Quantitative Set Analysis for Gene Expression

Homepage:

https://bioconductor.org/packages/3.20/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:

2.40.0-0,  2.36.0-0,  2.34.0-0,  2.32.0-0,  2.28.0-0,  2.26.0-0,  2.24.0-1,  2.24.0-0,  2.22.0-0, 

2.40.0-0,  2.36.0-0,  2.34.0-0,  2.32.0-0,  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:

>=2.66.0,<2.67.0

depends bioconductor-limma:

>=3.62.0,<3.63.0

depends r-base:

>=4.4,<4.5.0a0

depends r-emmeans:

depends r-fftw:

depends r-nlme:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-qusage

and update with::

   mamba update bioconductor-qusage

To create a new environment, run:

mamba create --name myenvname bioconductor-qusage

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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