RhythmicAlly: Your R and Shiny-Based Open-Source Ally for the Analysis of Biological Rhythms

J Biol Rhythms. 2019 Oct;34(5):551-561. doi: 10.1177/0748730419862474. Epub 2019 Jul 16.


Research on circadian rhythms often requires researchers to estimate period, robustness/power, and phase of the rhythm. These are important to estimate, owing to the fact that they act as readouts of different features of the underlying clock. The commonly used tools, to this end, suffer from being very expensive, having very limited interactivity, being very cumbersome to use, or a combination of these. As a step toward remedying the inaccessibility to users who may not be able to afford them and to ease the analysis of biological time-series data, we have written RhythmicAlly, an open-source program using R and Shiny that has the following advantages: (1) it is free, (2) it allows subjective marking of phases on actograms, (3) it provides high interactivity with graphs, (4) it allows visualization and storing of data for a batch of individuals simultaneously, and (5) it does what other free programs do but with fewer mouse clicks, thereby being more efficient and user-friendly. Moreover, our program can be used for a wide range of ultradian, circadian, and infradian rhythms from a variety of organisms, some examples of which are described here. The first version of RhythmicAlly is available on Github, and we aim to maintain the program with subsequent versions having updated methods of visualizing and analyzing time-series data.

Keywords: DAM; Drosophila; actogram; circadian; circatidal; period; periodogram; phase marking; power; time series.

Publication types

  • Letter
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Circadian Clocks*
  • Circadian Rhythm*
  • Data Analysis
  • Drosophila
  • Software / economics*
  • Software / supply & distribution