Code for performing analysis associated with Weiner et al., "Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data", Nature Communications (2024).
Snakemake pipelines are used to process data, run the PERT model for scRT inference, and do compute-intensive analysis tasks. For each unique dataset (i.e. fitness, sig_lines, etc), there is a snakemake rule file at rules/*.smk and a set of analysis scripts in the scripts/*/ folder. The output from these snakemake pipelines are used to create all main figures notebooks/main_figures/ and supplementary figures notebooks/supplementary_figures/. For a detailed instructions on how to use PERT for your own data, see the tutorials in the scdna_replication_tools github repository.
All source data needed to reproduce the figures (inputs to the jupyter notebooks), along with detailed descriptions of the file structure, are provided in our corresponding Zenodo submission. Please note that you will need to change input and output file paths if you wish to use this code and online source data to reproduce any of our analysis.