Thursday 6.3.2025 9:00-17:00

Friday 7.3.2025 9:00-17:00

This hands-on course introduces single-cell RNA-seq (scRNA-seq) data analysis concepts and R packages. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, cell type identification and differential expression analysis.

Practicalities

The course consists of lectures and exercises. Participants are requested to view the lecture videos prior to the course and test their knowledge with a set of questions. This gives you more time to reflect on the concepts so that you can use the classroom time more efficiently for discussions and exercises. The lecture videos are kindly provided by NBIS, the Swedish Node of ELIXIR (for more information, please see the section “Course materials” here below).

Participants are selected based on motivation description in the application form, and DPBM students have a priority. DPBM covers the course fee for their students.

This course is part of Single-Cell Course Week 2025 organized by the Doctoral Program in Biomedicine (DPBM). Please note that there is also Single Cell Omics Symposium on 13.3.2025 in Biomedicum Helsinki and Single-cell RNAseq data analysis using Chipster course on 4.-5.3.2025.

Prerequisites

You should have some experience in using R.

Content

Topics covered:

• quality control
• normalization
• removal of undesired sources of variation
• choosing variable genes
• dimensionality reduction
• clustering
• differential gene expression analysis
• integrating different datasets
• cell type identification

Trainers

Bishwa Ghimire, Anna Pirttikoski, Andrew Erickson, Franziska, Yafei Wang, Rene Wong Ramirez (University of Helsinki)

Course materials

The code for exercises will be available in Gitlab.

Before the course you need to watch the following lecture videos. The lectures are kindly provided by

• Åsa Björklund, Paulo Czarnewski and Olga Dethlefsen from National Bioinformatics Infrastucture Sweden (NBIS, ELIXIR-SE)
• Ahmed Mahfouz from Leiden University Medical Center, Netherlands

Module 2 Quality control: lectures 4, 6-8
Module 3 Normalization: lectures 1, 3-5
Module 4 Dimensionality reduction: lectures 1-5
Module 5 Data integration: lectures 1, 3-5
Module 6 Clustering: lectures 1-4, 8
Module 7 Differential expression: lectures 1-2, 4, 6
Module 8 Gene set analysis: lectures 1-3, 5
Module 9 Cell type prediction: lectures 1-5, 8

Slides and exercises will be shared during the course.

Price

Standard CSC on-site course prizing. Course participation fees for DPBM students are covered by Doctoral Program in Biomedicine (DPBM), who also selects the students to the course.

Important dates

• application deadline 12.2.2025
• selection results announced latest 26.2.2025