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https://github.com/bioconductor-source/zenith

https://github.com/bioconductor-source/zenith

Science Score: 26.0%

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    Found 4 DOI reference(s) in README
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Repository

Basic Info
  • Host: GitHub
  • Owner: bioconductor-source
  • Language: R
  • Default Branch: devel
  • Size: 6.87 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
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Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog

README.md


Gene set testing after dream analysis

`zenith()` performs gene set analysis on the result of differential expression using linear (mixed) modeling with [dream](https://doi.org/10.1093/bioinformatics/btaa687) by considering the correlation between gene expression traits. This package implements the [camera](https://www.rdocumentation.org/packages/limma/versions/3.28.14/topics/camera) method from the [limma](https://bioconductor.org/packages/limma/) package proposed by [Wu and Smyth (2012)](https://doi.org/10.1093/nar/gks461). `zenith()` is a simple extension of `limma::camera()` to be compatible with linear mixed models implemented in `variancePartition::dream()`.

Install

```r

Install package and dependencies

devtools::install_github("DiseaseNeuroGenomics/zenith") ```

Owner

  • Name: (WIP DEV) Bioconductor Packages
  • Login: bioconductor-source
  • Kind: organization
  • Email: maintainer@bioconductor.org

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Dependencies

.github/workflows/check-bioc.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc master composite
  • r-lib/actions/setup-r master composite
DESCRIPTION cran
  • R >= 4.2.0 depends
  • limma * depends
  • methods * depends
  • EnrichmentBrowser >= 2.22.0 imports
  • GSEABase >= 1.54.0 imports
  • Rdpack * imports
  • Rfast * imports
  • ggplot2 * imports
  • msigdbr >= 7.5.1 imports
  • progress * imports
  • reshape2 * imports
  • stats * imports
  • tidyr * imports
  • utils * imports
  • variancePartition >= 1.26.0 imports
  • BiocGenerics * suggests
  • BiocStyle * suggests
  • RUnit * suggests
  • edgeR * suggests
  • kableExtra * suggests
  • knitr * suggests
  • pander * suggests
  • rmarkdown * suggests
  • tweeDEseqCountData * suggests