Spatially resolved multiomics of human cardiac niches

Data processing and analysis for adult heart atlas, ver2
Processed data of sc/snRNAseq and Visium data are available for browsing and download via heartcellatlas.org

Contents

RNA

• QC
• Integration, Celltype annotation
• CCS

ATAC

• QC
• Peak calling
• Peak-to-Gene (ArchR)
• Dimensional reduction, integration (PeakVI)

Visium

• Cell2location (spatial mapping, NMF)
• Cell state spatial enrichment analysis
• Matching NMF-factors and histological annotations
• Nodal niche
• Immune niche
• Myocardial-stress niche
• SAN-RAGP

Citation

Spatially resolved multiomics of human cardiac niches https://doi.org/10.1038/s41586-023-06311-1

@article{Kanemaru2023,
  doi = {10.1038/s41586-023-06311-1},
  url = {https://doi.org/10.1038/s41586-023-06311-1},
  year = {2023},
  month = jul,
  publisher = {Springer Science and Business Media {LLC}},
  author = {Kazumasa Kanemaru and James Cranley and Daniele Muraro and Antonio M. A. Miranda and Siew Yen Ho and Anna Wilbrey-Clark and Jan Patrick Pett and Krzysztof Polanski and Laura Richardson and Monika Litvinukova and Natsuhiko Kumasaka and Yue Qin and Zuzanna Jablonska and Claudia I. Semprich and Lukas Mach and Monika Dabrowska and Nathan Richoz and Liam Bolt and Lira Mamanova and Rakeshlal Kapuge and Sam N. Barnett and Shani Perera and Carlos Talavera-L{\'{o}}pez and Ilaria Mulas and Krishnaa T. Mahbubani and Liz Tuck and Lu Wang and Margaret M. Huang and Martin Prete and Sophie Pritchard and John Dark and Kourosh Saeb-Parsy and Minal Patel and Menna R. Clatworthy and Norbert H\"{u}bner and Rasheda A. Chowdhury and Michela Noseda and Sarah A. Teichmann},
  title = {Spatially resolved multiomics of human cardiac niches},
  journal = {Nature}
}

Acknowledgments

This repository is dedicated to the memory of our dear friend and colleague Dr. Daniele Muraro who contributed to this analysis.