This repository contains the code for the analysis of single-cell RNA sequencing data from CD34+ bone marrow mononuclear cells of patients with chronic myelomonocytic leukemia (CMML) described in:
Ferrall-Fairbanks MC*, Dhawan A*, Johnson B, Newman H, Volpe V, Letson C, Ball M, Hunter AM, Balasis ME, Kruer T, Ben-Crentsil NA, Kroeger JL, Balderas R, Komrokji RS, Sallman DA, Zhang J, Bejar R, Altrock PM, Padron E. (2022) "Progenitor Hierarchy of Chronic Myelomonocytic Leukemia Identifies Inflammatory Monocytic-Biased Trajectory Linked to Worse Outcomes." Blood Cancer Discov. 2022 Nov 2; 3(6):536-553. doi: 10.1158/2643-3230.BCD-21-0217. PMID: 36053528. PMCID: PMC9627238.
This work was also presented at the 2021 American Society of Hematology (ASH) Annual Meeting on December 11 at 4pm. The full abstract for the oral presentation entitled "Single Cell Deconvolution of Myeloblasts Reveals Depletion of HSCs and Expansion of Inflammatory Granulocyte-Monocyte Progenitors (GMPs) Associated with Adverse Outcomes in Chronic Myelomonocytic Leukemia (CMML)" is available here.
Code is written in R and utilizes Linux platforms for some applications. If you are using this code and data in your research, please be sure to cite this paper.
The src folder contains subfolders with code for the primary and secondary analyses.
If you would like to improve this code or have any feedback, please file an issue or pull request or you can contact the maintainer at mferrall.fairbanks@bme.ufl.edu.