Here is code and additional files for analyzing the data in Single-molecule states link transcription factor binding to gene expression (DOI: https://doi.org/10.1101/2024.02.02.578660). The main analysis pipeline and supplementary scripts can be found here (https://github.com/GreenleafLab/amplicon-smf).
- Plasmid maps can be found in
plasmid_maps - Code for analyzing bulk RNA- and ATAC-seq data can be found in
atac_rna - Code for reproducing some of the panels of the paper (including single molecule matrices, ND model fits, AA model fits, and kinetic model fits) can be found in
paper_analyses