README.md

In DiscoRhythm: Interactive Workflow for Discovering Rhythmicity in Biological Data

DiscoRhythm - Discovering Rhythmicity

Overview

A summary of DiscoRhythm from Carlucci M. et al, 2020 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.

See the tutorial for details on usage of the web application and R package.

See DiscoRhythm on Bioconductor for more details.

Use the issue board 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 is installed, the DiscoRhythm container on Docker Hub 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

DiscoRhythm documentation built on Nov. 8, 2020, 7:32 p.m.