This code infers gene regulatory networks for early atrial and ventricular cardiomyocytes from human fetal multiomics data. The scRNA-seq and scATAC-seq human fetal data came from Ameen et. al. "Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and noncoding mutations in congenital heart disease" (https://doi.org/10.1016/j.cell.2022.11.028). CellOracle was used to infer the gene regulatory networks (https://doi.org/10.1038/s41586-022-05688-9). The inferred networks including both scRNA-seq and scATAC-seq data are stored in links.celloracle.links, and the networks were built in fetal_grn_building.ipynb. fetal_sc-rna-seq_preprocesing.ipynb requires the file human_6_8_12and19_merged_final_cleaned.h5ad, which can be downloaded as an rds file from https://doi.org/10.5281/zenodo.7063223 and then converted into a h5ad file.
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View Code? Open in Web Editor NEWGRNs for human fetal cardiac data