CalFluxTools: An R package for analysis of high-throughput calcium oscillation screening data

Patt, A. C.; Borschel, W. F.; Braisted, J.; Raza, D.; Wu, C.-K.; Farkondeh, A.; Strong, C.; Zhang, J.; Lee, E.; Traynor, B.; Mathe, E.

doi:10.64898/2026.09.15.751806

bioRxiv · 10.64898/2026.09.15.751806

CalFluxTools: An R package for analysis of high-throughput calcium oscillation screening data

Patt, A. C.·Borschel, W. F.·Braisted, J.·Raza, D.·Wu, C.-K.·Farkondeh, A.·Strong, C.·Zhang, J.·Lee, E.·Traynor, B.·Mathe, E.

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Abstract

Whole plate detection of calcium flux signals using fluorescence is a powerful technology for monitoring oscillatory activity of excitable cells in a high throughput fashion that sees broad applications in neurotoxicity and cardiotoxicity research. However, analysis of calcium oscillation profiles can output more than 60 peak kinetic parameters, which makes manual data analysis challenging. We have created the CalFluxTools R package, an automated pipeline for parsing plate data for 384 well plates, generating quality control metrics and plots, and performing data analysis, including T-tests, Z-score analysis, and machine learning prediction of compound toxicity values. CalFluxTools requires a plate map and experimental manifest that includes parameter filtration specifications, as well as data in the ".statall" format. CalFluxTools runs in less than a minute on a Macbook Pro with a 2.6 GHz 6-Core Intel Core i7 processor.

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Patt, A. C., Borschel, W. F., Braisted, J., Raza, D., Wu, C.-K., Farkondeh, A., Strong, C., Zhang, J., Lee, E., Traynor, B., Mathe, E.. 2026-09-21. CalFluxTools: An R package for analysis of high-throughput calcium oscillation screening data. https://doi.org/10.64898/2026.09.15.751806

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