This repository contains Matlab files used in the manuscript "Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos"
Shaded error bars were generated using: Rob Campbell (2023). raacampbell/shadedErrorBar (https://github.com/raacampbell/shadedErrorBar), GitHub Beeswarm plots were generated using: Jonas (2023). plot spread points (beeswarm plot) (https://www.mathworks.com/matlabcentral/fileexchange/37105-plot-spread-points-beeswarm-plot), MATLAB Central File Exchange.
signal extraction contains codes for segmentation and signal extraction
plot generation includes code used to generate plots
modeling_4_sites contains the code to create the equilibrium binding model
viterbi_on_off contains the code used to generate the HMM traces