A kinetics-based model of hematopoiesis reveals extrinsic regulation of skewed lineage output from stem cells - code & data repository

Code & Data Repository Description This repository contains the scripts, source and scRNA-seq data to generate the main and supplementary figures within the manuscript Linking stem cell heterogeneity to reconstitution kinetic through in-depth single-cell analyses of clonally-derived hematopoietic systems. scRNA-seq datasets Single-cell RNA sequencing data derive from five single-HSC-derived murine hematopoietic systems, as well as two polyclonal controls. The resulting clonally-resolved hematopoietic bone marrow atlas (scBM_atlas.rds) consists of 76,863 high-quality cells and covers all major hematopoietic cell types, including differentiation tracks (slingshot.rds) from the most immature HSCs to all lineage-committed progenitors (HSPCs.rds) and their continued maturation into blood and immune cells. Manuscript source code and tabular data This folder contains the code and manuscript source data for the manuscript. Quick Start: Setting Up Your R Project To ensure all scripts run correctly, you must set up your R Project (.Rproj) in the root directory of this repository. The scripts are written assuming that the "Manuscript" and "scRNA-seq Data" folders are located directly inside your working directory, i.e. the project folder should look like this: My_Analysis/