Single-Cell RNA-Seq Data Analysis
Description
This workshop will introduce the best practice bioinformatics methods for analyzing single cell RNA-seq data via a series of lectures and computer practicals (using R or Python according to each student’s preference). The total course duration is 5 days, which includes 4 days of lectures and exercises followed by a "Bring Your Own Data" (BYOD) day where you get to practice your skills on a dataset of your choosing.
Topics covered will include:
- Overview of the current scRNAseq technologies
- Basic overview of pipelines for processing raw reads into expression values
- Quality control and normalization
- Dimensionality reduction techniques
- Data integration and batch correction
- Differential gene expression
- Clustering techniques
- Cell type prediction
- Trajectory inference analysis
- Comparison of Seurat, Bioconductor and Scanpy toolkits
Upcoming Training Instances
No upcoming training instances.
Content Providers
Learning Outcomes
Upon completion of this course, you will be able to run analysis on your own data, select appropriate analysis methods and interpret the results.
Structure & Duration
The course comprises 5 full days of lectures, practical exercises and analysis of own data ("Bring your own data" = BYOD). The lectures and exercises are on 4 consecutive days. The BYOD session may be the next day or at a later time point depending on the chosen format each year.
Prerequisites & Technical Requirements
Prior Knowledge
The following is a list of skills required for being able to follow the course and complete the exercises:
- You are familiar with basic UNIX command line (bash)
- You are familiar with R and/or Python
- You understand the basics of NGS technologies
- You are familiar with analyses of bulk RNA-sequencing data
Technical Requirements
You will need to have full access to your computer (admin permissions).
Audience & Keywords
Target Audience
Keywords
Course Team
Authors
- Jennifer Fransson · NBIS, SciLifeLab, Uppsala University · jennifer.fransson@scilifelab.se
- Susanne Reinsbach · NBIS, SciLifeLab, Chalmers University of Technology · susanne.reinsbach@scilifelab.se
Contributors
- Åsa Björklund · NBIS, SciLifeLab, Chalmers University of Technology
- Roy Francis · NBIS, SciLifeLab, Uppsala University
- Aditya Singh · NBIS, SciLifeLab, Chalmers University of Technology
- Stedan Ebmeyer · NBIS, SciLifeLab, Chalmers University of Technology
- Yuan Li · NBIS, SciLifeLab, Lund University
- Fariba Roshanzamir · NBIS, SciLifeLab, Chalmers University of Technology
Past Course Instances
Single-Cell RNA-Seq Data Analysis
April 13, 2026 09:00 – April 27, 2026 17:00
Single-Cell RNA-Seq Data Analysis
March 31, 2025 09:00 – April 03, 2025 17:00
Single Cell RNA-Seq Data Analyses Workshop
February 12, 2024 09:00 – February 16, 2024 17:00
Activity log
