Code for bulk RNA-seq and single-cell RNA-seq analyses in: "Medullary cavity expansion is mediated by distinct cell populations during fetal bone development"

This repository contains custom R scripts used for bulk RNA sequencing (bulk RNA-seq) and single-cell RNA sequencing (scRNA-seq) analyses in the study: Sumiya et al., "Medullary cavity expansion is mediated by distinct cell populations during fetal bone development". The repository includes code used to generate several figures in the manuscript as well as scripts used for the analysis of scRNA-seq datasets and reanalysis of publicly available data. The repository is organized into two main directories: bulkRNAseq_code/R scripts and processed count tables used for bulk RNA-seq analyses corresponding to specific figures in the manuscript. scRNAseq_code/R scripts used for single-cell RNA-seq analysis of fetal bone and fracture datasets, as well as reanalysis of publicly available scRNA-seq data. The scripts were written in R and primarily use the Seurat package for scRNA-seq analysis. For scripts reanalyzing public datasets, the input data can be obtained from the Gene Expression Omnibus (GEO). Public dataset used for reanalysis:GSE154247 Processed Seurat objects required for reproduction of the analyses are included where appropriate. All scripts were tested with R version 4.5.1.