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DiscoRhythm-package.Rd 100644 1 kb
PeriodDetection_range.Rd 100644 0 kb
checkJTKperiod.Rd 100644 0 kb
checkPeriod.Rd 100644 1 kb
discoApp.Rd 100644 1 kb
discoBatch.Rd 100644 4 kb
discoCheckInput.Rd 100644 1 kb
discoColors.Rd 100644 1 kb
discoDFtoSE.Rd 100644 2 kb
discoDesignSummary.Rd 100644 1 kb
discoGetSimu.Rd 100644 1 kb
discoODAexclusionMatrix.Rd 100644 1 kb
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discoPCA.Rd 100644 1 kb
discoPCAgetOutliers.Rd 100644 1 kb
discoParseMeta.Rd 100644 1 kb
discoPeriodDetection.Rd 100644 1 kb
discoQC.Rd 100644 3 kb
discoShinyHandler.Rd 100644 0 kb
fisherExact.Rd 100644 0 kb
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README.md
# DiscoRhythm - Discovering Rhythmicity <img src="inst/app/www/disco_128.png" align="right" width="120" /> ![platforms](https://bioconductor.org/shields/availability/3.10/DiscoRhythm.svg) ![build](https://bioconductor.org/shields/build/release/bioc/DiscoRhythm.svg) ![in Bioc](https://bioconductor.org/shields/years-in-bioc/DiscoRhythm.svg) [![](https://img.shields.io/badge/doi-10.1093/bioinformatics/btz834-green.svg)](https://doi.org/10.1093/bioinformatics/btz834) ## Overview A summary of DiscoRhythm from *[Carlucci M. et al, 2020](https://doi.org/10.1093/bioinformatics/btz834)* is presented below. ![](inst/DiscoRhythm_Figure1.png) > DiscoRhythm is available as a web application or an R/Bioconductor package for estimating phase, amplitude, and statistical significance using four popular approaches to rhythm detection (Cosinor, JTK Cycle, ARSER, and Lomb-Scargle). [...] Informative visualizations, interactive modules for quality control, dimensionality reduction, periodicity profiling, and incorporation of experimental replicates make DiscoRhythm a thorough toolkit for analyzing rhythmicity. ----------------------------------------------------- ## Getting Started The web application can be accessed on the [DiscoRhythm public server](https://mcarlucci.shinyapps.io/discorhythm/). See the [tutorial](https://bioconductor.org/packages/release/bioc/vignettes/DiscoRhythm/inst/doc/disco_workflow_vignette.html) for details on usage of the web application and R package. See [DiscoRhythm on Bioconductor](https://bioconductor.org/packages/release/bioc/html/DiscoRhythm.html) for more details. Use the [issue board](https://github.com/matthewcarlucci/DiscoRhythm/issues) to provide feedback on DiscoRhythm (feature requests, bugs, and further questions). ### R Package Installation For local usage of DiscoRhythm, install the R package from Bioconductor: ``` if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("DiscoRhythm") ``` Or install the latest version from GitHub: ``` library(devtools) install_github("matthewcarlucci/DiscoRhythm", build_vignettes=TRUE) ``` ### Usage with Docker If [docker](https://docs.docker.com/install/) is installed, the [DiscoRhythm container on Docker Hub](https://hub.docker.com/r/mcarlucci/discorhythm) can be used to run the DiscoRhythm web application. ### Citation >Matthew Carlucci, Algimantas Kriščiūnas, Haohan Li, Povilas Gibas, Karolis Koncevičius, Art Petronis, Gabriel Oh, DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity, *Bioinformatics*, Volume 36, Issue 6, 15 March 2020, Pages 1952–1954, [https://doi.org/10.1093/bioinformatics/btz834](https://doi.org/10.1093/bioinformatics/btz834)