CIRCADA: Shiny Apps for Exploration of Experimental and Synthetic Circadian Time Series with an Educational Emphasis
Journal of Biological Rhythms
Circadian rhythms are daily oscillations in physiology and behavior that can be assessed by recording body temperature, locomotor activity, or bioluminescent reporters, among other measures. These different types of data can vary greatly in waveform, noise characteristics, typical sampling rate, and length of recording. We developed 2 Shiny apps for exploration of these data, enabling visualization and analysis of circadian parameters such as period and phase. Methods include the discrete wavelet transform, sine fitting, the Lomb-Scargle periodogram, autocorrelation, and maximum entropy spectral analysis, giving a sense of how well each method works on each type of data. The apps also provide educational overviews and guidance for these methods, supporting the training of those new to this type of analysis. CIRCADA-E (Circadian App for Data Analysis–Experimental Time Series) allows users to explore a large curated experimental data set with mouse body temperature, locomotor activity, and PER2::LUC rhythms recorded from multiple tissues. CIRCADA-S (Circadian App for Data Analysis–Synthetic Time Series) generates and analyzes time series with user-specified parameters, thereby demonstrating how the accuracy of period and phase estimation depends on the type and level of noise, sampling rate, length of recording, and method. We demonstrate the potential uses of the apps through 2 in silico case studies.
circadian rhythms, biological oscillations, data analysis, discrete wavelet transform, periodogram, mathematical analyses, Shiny app
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Licensed to Smith College and distributed CC-BY under the Smith College Faculty Open Access Policy.
Cenek, Lisa; Klindziuk, Liubou; Lopez, Cindy; McCartney, Eleanor; Burgos, Blanca Martin; Tir, Selma; Harrington, Mary E.; and Leise, Tanya L., "CIRCADA: Shiny Apps for Exploration of Experimental and Synthetic Circadian Time Series with an Educational Emphasis" (2020). Psychology: Faculty Publications, Smith College, Northampton, MA.
Mathematics Commons, Psychiatry and Psychology Commons, Statistics and Probability Commons
Peer reviewed accepted manuscript.