Analysis of Single-Cell RNA-seq Data with Python
Hands-on workshop series on single-cell RNA-seq analysis using Python and Scanpy.
Instructor: Yura Song, PhD and Zian Liu, PhD
Term: Spring
Location: Université Libre de Bruxelles, Brussels, Belgium
Overview
Workshop series organised as part of the Bioinformatics Forum at Université Libre de Bruxelles (ULB), introducing practical analysis workflows for single-cell RNA-seq data using Python.
The workshops are based on PBMC single-cell datasets and focus on reproducible analysis workflows using Scanpy and related Python tools.
Topics covered
- Quality control and filtering
- Normalisation and preprocessing
- Dimensionality reduction
- Clustering and annotation
- Differential gene expression analysis
- Gene regulatory network inference with SCENIC
- Downstream biological interpretation
Course materials
Schedule
| Week | Date | Topic | Materials |
|---|---|---|---|
| 1 | Mar 2026 | Introduction to single-cell RNA-seq analysis with Python Hands-on introduction to Scanpy-based analysis of PBMC single-cell RNA-seq data, including quality control, preprocessing, dimensionality reduction and clustering. | |
| 2 | Jun 2026 | Downstream analysis of single-cell RNA-seq data Follow-up workshop focusing on downstream analysis including differential gene expression analysis, pathway analysis and gene regulatory network inference using SCENIC. |