:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-qusage' .. highlight: bash bioconductor-qusage =================== .. conda:recipe:: bioconductor-qusage :replaces_section_title: :noindex: qusage\: Quantitative Set Analysis for Gene Expression :homepage: https://bioconductor.org/packages/3.18/bioc/html/qusage.html :license: GPL (>= 2) :recipe: /`bioconductor-qusage `_/`meta.yaml `_ :links: biotools: :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 \(steven.kleinstein\@yale.edu\) .. conda:package:: bioconductor-qusage |downloads_bioconductor-qusage| |docker_bioconductor-qusage| :versions: .. raw:: html
2.36.0-02.34.0-02.32.0-02.28.0-02.26.0-02.24.0-12.24.0-02.22.0-02.20.0-0 ``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`` .. raw:: html
:depends bioconductor-biobase: ``>=2.62.0,<2.63.0`` :depends bioconductor-limma: ``>=3.58.0,<3.59.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-emmeans: :depends r-fftw: :depends r-nlme: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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: (see `bioconductor-qusage/tags`_ for valid values for ````) .. |downloads_bioconductor-qusage| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-qusage.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-qusage :alt: (downloads) .. |docker_bioconductor-qusage| image:: https://quay.io/repository/biocontainers/bioconductor-qusage/status :target: https://quay.io/repository/biocontainers/bioconductor-qusage .. _`bioconductor-qusage/tags`: https://quay.io/repository/biocontainers/bioconductor-qusage?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-qusage/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-qusage/README.html