hematopoiesis

The data preprocessing pipeline for the VISION project (for mouse data)

HemaHier: Chain-Conditioned Ordinal Hierarchies for Lineage-Aware Bone-Marrow Cytology

Python code to [Buggenthin2017]

The data preprocessing pipeline for the VISION project (for human data)

End-to-end single-cell RNA-seq analyses on public datasets — 10 reproducible projects in Scanpy & Seurat covering integration, trajectory inference, cell-cell communication, and method benchmarks.

Computational analysis of gene expression profiles to uncover key biomarkers distinguishing bone marrow and peripheral blood CD34+ stem cells, with applications in diagnostics and stem cell transplantation.

Single-cell RNA-seq workflows for tumour microenvironment profiling and haematopoietic differentiation using Scanpy, Harmony, Leiden clustering, differential expression and diffusion pseudotime.

Pilot analyses for trajectory-aware regulatory representation learning in hematopoietic differentiation.

Interactive scRNA-seq fate mapping of human hematopoietic stem/progenitor cells using Scanpy, CellRank, GPCCA and Streamlit.

This repository contains the code used for the project "Stochastic modeling of clonal memory effects on population growth of dividing and differentiating cells".

Integrated scRNA-seq and bulk RNA-seq analysis of iPSC-derived hematopoietic stem cell differentiation (Ng et al. 2025 + GSE232710)

Repo for the script used in Nicolet et al. 2021 paper on the study of circRNA in megakaryoid and erythroid differentiation

End-to-end scRNA-seq analysis of human bone marrow (BMMC): clustering and annotation, a dimensionality-reduction benchmark, pathway, trajectory, cell-cell communication and deconvolution.