scXploringTheNiche

Single-cell eXploring the Bone Marrow Niche

This is a collection of Rmarkdown files associated with analysis of scRNA-seq expression matricies generated in various published studies

Depends on:

• make
• curl
• R

Recapitulation of analysis presented by Baryawno et al. using Seurat v4.1.0 and Tidyverse v1.3.1 to characterize the mouse bone marrow stroma under homeostasis conditions.

Before starting the analysis, run make prep-dataset-baryawno-homeostasis to download the required 10X output files from the NCBI's GEO repository for GSE128423.

• scRnaTaxonomyOfBmStromaHomeostasis.Rmd

Recapitulation of analysis presented by Baryawno et al. using Seurat v4.1.0 and Tidyverse v1.3.1 to characterize the bone marrow stroma of MLL transplanted mice.

Before starting the analysis, run make prep-dataset-baryawno-leukemic to download the required 10X output files from the NCBI's GEO repository for GSE128423.

• scRnaTaxonomyOfBmStromaControlVsLeukemic.Rmd