Introduction

This is all code used by Ranade et. al. for the submission "Single Cell Epigenetics Reveal Cell-Cell Communication Networks in Normal and Abnormal Cardiac Morphogenesis" to [awaiting journal decision].

Manuscript is currently available on bioRxiv: DOI 2022.07.25.501458

Analysis

All data was processed and analyzed using Cellranger, Seurat, ArchR and supporting packages as detailed in provided scripts. See 10x Genomics documenation for Cellranger and Cellranger ATAC usage.

Analysis order:

1. Process scRNA/scATAC 10x Genomics Cellranger v5.0.1 & Cellranger-atac v1.2.0 pipelines:
   • cellranger count & cellranger-atac count
   • cellranger aggr
2. Process and analyze scRNA seq data with Seurat v3 and v4 using scripts scRNA-seq/*/ folder:
3. Process and analyze scATAC data with ArchR v1.0.1 using scripts in scATAC-seq/* folder

Please flag any issues and contact Dr. Sanjeev Ranade at sanjeev.ranade@gladstone.ucsf.edu.

Data Availability

All sequencing data is available via GEO/SRA: GSE198567