checkpoint files scRNASeq analysis

Analysis of a publicly available dataset, generated for teaching purposes by Federico La Manna, basing on the following original research article: "Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging" (CC BY-NC-ND 4.0) Cell, Volume 187, Issue 12, 6 June 2024, Pages 3120-3140.e29, https://doi.org/10.1016/j.cell.2024.04.013 Shovik Bandyopadhyay 1 2, Michael P. Duffy 3 14, Kyung Jin Ahn 4 14, Jonathan H. Sussman 2 8, Minxing Pang 5, David Smith 6, Gwendolyn Duncan 7, Iris Zhang 9, Jeffrey Huang 7, Yulieh Lin 3, Barbara Xiong 2 8, Tamjid Imtiaz 7, Chia-Hui Chen 4, Anusha Thadi 4, Changya Chen 4, Jason Xu 2 8, Melissa Reichart 3, Zachary Martinez 4, Caroline Diorio 4 13, Chider Chen 10 1 Cellular and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA 2 Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA 3 Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA 4 Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA 5 Applied Mathematics & Computational Science Graduate Group, University of Pennsylvania, Philadelphia, PA, USA 6 Center for Single Cell Biology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA 7 Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA 8 Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA 9 Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, USA 10 Department of Oral and Maxillofacial Surgery/Pharmacology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA 11 Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA 12 Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA 13 Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA