This repository also contains the code and data to recreate the figures, tables, performs trans-eQTL hotspot analysis, cell-cycle stage assignment, raw data processing, and additional links to generated data.
Sequencing data for each single-cell experiment is available on the SRA PRJNA1049497.
see load_all_data.R for the main post analysis script that generates the figures and tables, and performs the trans-eQTL hotspot analysis.
To run these scripts one needs to first download the processed data from Zenodo and extract it into the data directory. The data can be downloaded here.
see README_DATA.md for a detailed description of the organization and sheets contained within the hotspot annotation tarball File S1.
see cell_cycle_annotation.R for the cell-cycle stage assignment script.
see numbers_final for scripts that generate all the numbers found in the maintext.
see raw_data for the raw data processing script.
see pre_processing_repository to access the code used to run the HMM and eQTL mapping analysis.
see R_dependencies for the R version and list of packages used for this analysis.