Chronomics analysis toolkit (CATkit)

Abstract

Chronomics, and the study of biological rhythms, is a rapidly growing area of study. As biological researchers transition to awareness of the impact biological oscillators have on experimental outcomes, and the need to design experiments around genetic, molecular, physiological, and behavioral rhythms, there is increasing need to identify and characterize rhythmicity. There is a corresponding increase in demand for accessible software tools to analyze data for rhythms, both macroscopically and quantitatively. The chronomics analysis toolkit (CATkit), an R package for analysis of periodicities in time series, is a free and open source suite of rhythm analysis tools that runs on UNIX, Windows, and Macintosh platforms. It is particularly well suited to the often scarce, frequently noisy, biological data, and is also applicable to long and/or denser records. CATkit includes a variety of tools, providing visualization and inspection tools to aid in determining whether data meet key assumptions for analysis; as well as quantitative assessment, by cosinor, of mean, amplitude and phase at an assumed period (or periods), with a measure of uncertainty for each parameter.

Keywords:

• chronobiology
• rhythm
• period
• R
• CATkit, Cosinor

Funding

This work was supported by the Office of the Vice President for Research at the University of Minnesota (CJLG); Halberg Chronobiology Fund (GC).