This repository contains the code used to generate figures and perform analysis for the manuscript titled "Mapping the Cellular Biogeography of Human Bone Marrow Niches Using Single-Cell Transcriptomics and Proteomic Imaging". The data from this manuscript is interactively browsable through our Vitessce-based platform.

Data Availability
Raw and processed scRNA-Seq data can be accessed through GSE253355. Raw and processed CODEX data can be accessed through our repository on FigShare.

Citation
If you are using code or pipelines from this repository, please consider citing our associated article:

Bandyopadhyay, S., Duffy, M. P., Ahn, K. J., Sussman, J. H., Pang, M., Smith, D., Duncan, G., Zhang, I., Huang, J., Lin, Y., Xiong, B., Imtiaz, T., Chen, C.-H., Thadi, A., Chen, C., Xu, J., Reichart, M., Martinez, Z., Diorio, C., . . . Tan, K. Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging. Cell. 2024. https://doi.org/10.1016/j.cell.2024.04.013

Figure Manifest
General scRNA-Seq Analysis Figure 1B-D, S1C-F,Figure 2A-C, Figure 2G-H, Figure S3A-C, Figure S3E , Supplemental Table S2, Figure 3A, Figure 5E, Figure S7B- scRNA_Seq_Analysis/Step1_AtlasGeneration_and_Figures/SB_Manuscript_scRNA_Analysis.R

scRNA-Seq Inflammation Analysis Figure S2A-D scRNA_Seq_Analysis/Step1.2_MapExternalDatasets/Inflammation_Comparison_ForManuscript.R

CytoTRACE Analysis Figure 2D – scRNA_Seq_Analysis/Step1.1_Run_CytoTRACE/CytoTrace_BM.R

External Dataset Mapping Figure 2I, Supplemental Figure S4A scRNA_Seq_Analysis/Step1.2_MapExternalDatasets/Map_MSC_Datasets_Manuscript.R scRNA_Seq_Analysis/Step1.2_MapExternalDatasets/Integrate_Mapped_Datasets_ForManuscript_v3.R

Figure S4B - scRNA_Seq_Analysis/Step1.2_MapExternalDatasets/Bandyopadhyay_Jardine_integration_ForManuscript.R

CellChat Analysis Figure S4A, S4E, S8B - scRNA_Seq_Analysis/Step2_CellChat/CellChat_ForMaunscript.R

CODEX Cell Type Annotation Figure 4C-4D - CODEX_Analysis/Step3_AnnotateCells/NBM_CODEX_Atlas_Combined_Step3_AnnotateCells.R

CODEX MSC Subset Manual Annotation and Distance Analysis Figure S6E - CODEX_Analysis/Step1_CreateSeuratObjs/Fibro_Osteo_MSC_Create_Seurat.R Figure 4E - CODEX_Analysis/Step8_Distance_Analysis/MSC_Distance_Analysis_VlnPlots.R

CODEX NBM Neighborhood Analysis Figure 5A, 5D, S7D-E - CODEX_Analysis/Step4_NBM_NeighborhoodAnalysis/NeighborhoodAnalysis_Step4_FINAL.R CODEX_Analysis/Step4_NBM_NeighborhoodAnalysis/Combined_NeighborhoodAnalysis.ipynb Neighborhood Enrichment Stats - CODEX_Analysis/Step4_NBM_NeighborhoodAnalysis/Hypergeometric_Statistics_NBM.R

CODEX Structure Distance Analysis Figure 6A-E, S9B, S11D - CODEX_Analysis/Step8_Distance_Analysis/Plot_Rank_Data_ForManuscript.R

CODEX NSM Annotation Figure 7A, S10A, S10D-E, also needed for 7B-C CODEX_Analysis/Step5_NSM_ReferenceMapping/ReferenceMap_NSM_ForManuscript.R

CODEX AML Blast Mapping Figure 7B CODEX_Analysis/Step6_AML_ReferenceMapping/RefMap_AML_ForManuscript_Final.R CODEX_Analysis/Step6_AML_ReferenceMapping/SpatialJoin_AML.R

CODEX AML Analysis Figure 7C-D, 7F-G, S11B,S11D, S11E-G - CODEX_Analysis/Step7_NeighborhoodAnalysis_AML/AML_NSM_neighborhood_analysis_ForManuscript.R Neighborhood Enrichment Stats - CODEX_Analysis/Step7_NeighborhoodAnalysis_AML/Hypergeometric_Statistics_AML.R

CODEX NSM Neighborhood Analysis Figure S10D-E - CODEX_Analysis/Step5_NSM_ReferenceMapping/NSM_NBM_Correlation.R CODEX_Analysis/Step5_NSM_ReferenceMapping/NSM_Only_NeighborhoodAnalysis-.ipynb Neighborhood Enrichment Stats - CODEX_Analysis/Step5_NSM_ReferenceMapping/Hypergeometric_Statistics_NSM.R

Integrated Analysis Figure 5F Integrated_Analysis/Integrate_CellChat_and_NeighborhoodAnalysis_ForManuscript_v2.R

Figure S5F-G Integrated_Analysis/RNA_Protein_Correlation_Median_ForManuscript.R

Ligand-Receptor CODEX Analysis Figure S8C CODEX_Analysis/Step9_LR_Analysis/LR_Distance_Analysis_ForManuscript.R

Acknowledgments
Major contributions to this codebase are from Shovik Bandyopadhyay, Jonathan Sussman, Minxing Pang, David Smith, Derek Oldridge, and Kai Tan. We also acknowledge and greatly appreciate the Children's Hospital of Philadelphia's Research IS team, especially John Daniels, for their tremendous support in HPC implementation of this work.