There are many programs that can do Cosinor analysis. Does anyone recommend a particular software, or is it best to do the analysis manually on Prism (Graphpad)?
From a preliminary search, I came across papers that used:
- Cosinor (V1.1) R package
- Matlab
- Cosinor software (Boise State University)
- Cosinor V3.0.02 (University of Barcelona)
- CSR 3.0.2
Thank you,
Maryam
Thanks. I found the popular answer in the following post to be helpful (https://www.researchgate.net/post/Does_anyone_know_a_method_of_cosinor_analysis).
Thank you, Saurav Saha and Zeeshan Khan
. I opted for using Prism and doing a nonlinear curve fit, using this equation:Y=Baseline+Amplitude*cos(Frecuency*X+Phaseshift)
However, the calculated acrophase (phaseshift) is very different from the observed peak time on the curve. Do you know why?
Dear Maryam
I would like to suggest you that for the cosinor analysis purpose you will be using circwave software. In this software you should analysis your individual time point data either fitter or not. If it will be fitted then it indicate that proper rhythm will be showed in a pictorial format.
The calculated acrophase (phaseshift) is very different from the observed peak time on the curve because ± value should be calculated with your real acrophase value. Then both value might be same.
I think it will be help to you.
Thanks.
I recommend the (free) Cosinor software (Boise State University) that can be downloaded at circadian.org. It's pretty simple to use and the creator of the program (Prof. Refinetti) is quite supportive and happy to help. This software has been very useful in making sense of my circadian rhythm data for my PhD thesis (available on researchgate for your perusal).
For bibliography and other information, please, go to the original source: http://halbergchronobiologycenter.umn.edu/home/dr-cornelissen-director
Thanks everyone. I have also found Chronos-fit to be great for circadian parameter calculations and curve fitting, though I advise exporting the fitted curve values and graphing elsewhere. It's free, but you have to request the activation file from the authors (or possibly anyone who has the file?).
You may also have a look here:
https://academic.oup.com/bioinformatics/article-abstract/36/4/1208/5582266?redirectedFrom=fulltext
The code/software is freely available.
You can take a look at the Python implementation called CosinorPy. You can install the package using pip (pip install CosinorPy) or download it from https://github.com/mmoskon/CosinorPy
The package is also described in Article CosinorPy: a Python package for cosinor‑based rhythmometry
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