https://github.com/matthewcarlucci/discorhythm

An R Package for Discovering Rhythmicity in Biological Data with an Interactive Web Interface
https://github.com/matthewcarlucci/discorhythm

bioconductor data-visualization oscillations package r rhythm-detection webapp

Last synced: 8 days ago
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An R Package for Discovering Rhythmicity in Biological Data with an Interactive Web Interface

• Host: GitHub
• URL: https://github.com/matthewcarlucci/discorhythm
• Owner: matthewcarlucci
• Created: 2019-04-05T00:21:05.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2022-03-07T22:28:44.000Z (over 2 years ago)
• Last Synced: 2024-09-20T15:26:20.683Z (about 2 months ago)
• Topics: bioconductor, data-visualization, oscillations, package, r, rhythm-detection, webapp
• Language: R
• Homepage: https://bioconductor.org/packages/DiscoRhythm
• Size: 2.29 MB
• Stars: 12
• Watchers: 4
• Forks: 2
• Open Issues: 5
• Metadata Files:
  • Readme: README.md

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README

        

# DiscoRhythm - Discovering Rhythmicity 

![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)