Introduction to analysis of single cell RNA data

Dates & Times: Wednesday 3rd June 10:00-17:00, Thursday 4th June 09:00-16:00

Location: Seminar room 0.03, Hamburg Center for Translational Immunology (HCTI), Building N25, UKE

Instructor: Dr. Maksims Fiosins, Institute of Medical Systems Bioinformatics, UKE

Language: English

Prerequisites: Basics of molecular biology, basic IT knowledge (no programming skills required).

Description: This two-day workshop provides a structured introduction to single-cell RNA-sequencing (scRNA-seq) analysis, combining theoretical foundations with practical exercises to help participants understand and interpret scRNA-seq data. The theoretical components will present the complete conceptual workflow—from experimental design considerations to raw data processing, quality control, normalization, dimensionality reduction, clustering, and data integration. These sessions will guide attendees in evaluating scRNA-seq datasets, understanding the reasoning behind each part of the workflow, and selecting methods that lead to reliable biological insights.
The practical components translate these concepts into hands-on skills through guided exercises, primarily in Google Colab. Participants will become familiar with the Nextflow workflow manager, explore nf-core pipelines such as nf-core/scrna and nf-core/scdownstream, and learn to understand the structure and meaning of the results. They will also review data integration using the Semares platform and Cellxgene explorer, and perform custom downstream analyses in Scanpy. AI-assisted coding support will help attendees create their own analysis functions in Python and develop custom analysis, even with limited programming experience. The workshop will enable participants to complete an end-to-end analysis and prepare them to apply modern scRNA-seq methodologies to their own datasets.

Topics:

  • Overview of scRNA-seq technologies
  • scRNA raw data processing
  • scRNA-seq processing workflows
  • Downstream Single-Cell Analysis

Registration for this workshop will open soon