# DiscoRhythm - Discovering Rhythmicity <img src="inst/app/www/disco_128.png" align="right" width="120" />
[](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.
> 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)
