This code provides the scripts used to analyse growth curves on a plate reader from [1] and [2]. It initially used a pandas panel data object, but is now gradually being converted to use a dictionary.
The main functions are contained in the file core/plate_reader_tools.py
Scripts to generate analysis and figures are in the scripts/Ben/ folder The script used for ref [1] are listed in PKA_evolution_fig_notes.txt Also in the scripts/Ben folder is std_libraries.py which can be run at the beginning of a script to load all necessary libraries.
Example data is contained in scripts/templates. Data for [1] is on figshare.
The code was primarily run on a windows environment using conda (see environment.yml) but should work with Linux as well.
[1] Heineike, B., and El-Samad, H. (2021). Paralogs in the PKA regulon traveled different evolutionary routes to divergent expression in budding yeast. Front. Fungal Biol. 2. doi:10.3389/ffunb.2021.642336.
[2] Kundert, K., Lucas, J. E., Watters, K. E., Fellmann, C., Ng, A. H., Heineike, B. M., et al. (2019). Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Nat Commun 10, 2127. doi:10.1038/s41467-019-09985-2.
- Benjamin Heineike heineike02
This project is licensed under the MIT License - see the LICENSE.md file for details