Replication package for: Single-cell multi-omic analysis reveals principles of transcription-chromatin interaction during embryogenesis

This dataset and associated code enable the replication of all key results described in the manuscript "Single-cell multi-omic analysis reveals principles of transcription-chromatin interaction during embryogenesis" by Bhardwaj et al. (2024). Description of files/folders: config_files: This folder contains the configuration parameters for the preprocessing of raw fastq files from GEO, which can be plugged into our preprocessing workflow (scChICflow). It also contains config files for pyGenomeTracks, to plot our signals over a genomic region. source_data: contains .txt and .RDS formatted files, which can be loaded in R to reproduce our figures. figure-01.Rmd until figure-04.Rmd files: contain code to reproduce our key results from both main and supplementary figures, in Rmarkdown format. functions_and_variables.R: loads the R packages needed to reproduce the figures (please pre-install them), along with some custom plotting functions. Additionally, our raw data (.fastq format), count tables (.h5ad format), signal tracks (.bigwig format) and peaks/regions files (.bed format) are openly available on GEO, with accession No. GSE265874. GEO files are not necessary to reproduce the above results. For more information, please feel free to contact the lead author.