Chapter 1 Introduction

This tutorial presents the analysis code for a spatiotemporal atlas of human osteo-hematopoietic niches across fetal development, adulthood, and aging. The project integrates single-cell RNA sequencing and spatial transcriptomic data to characterize the cellular composition of the bone marrow microenvironment.

The code covers data preprocessing, cell filtering, normalization, dimensionality reduction, clustering, and cell annotation. Downstream workflows include differential gene expression analysis, gene signature scoring, cell population comparisons, trajectory analysis, and cellcell communication analysis. Spatial analysis scripts cover cell population mapping and visualization of tissue-associated gene expression patterns.