In this course, you will learn how to analyse single-cell RNA-seq data using the Seurat single cell tools integrated in the easy-to-use Chipster software. The exercises and course data are based on the Seurat guided analyses "Guided tutorial - 2700 PBMCs" and "Stimulated vs Control PBMCs".
This course contains two types of lecture videos: short lectures on each topic by trainers from CSC (ELIXIR-FI), and more in-depth lectures by Paulo Czarnewski (NBIS / ELIXIR-SE), Ahmed Mahfouz (LUMC / ELIXIR-NL) and Jules Gilet (ELIXIR-FR).
You will learn the following topics, and how to perform these steps in the Chipster software:
- perform quality control and filter out low quality cells
- normalize gene expression values
- scale data and remove unwanted sources of variation
- select highly variable genes
- perform dimensionality reduction (PCA, tSNE, UMAP, CCA)
- cluster cells
- find marker genes for a cluster
- integrate two samples
- find conserved cluster marker genes for two samples
- find genes which are differentially expressed between two samples in a cell type specific manner
- visualize genes with cell type specific responses in two samples
"It is so nice to be able to do the whole workflow in Chipster, compared to the old model, where I had to transfer the tsv file to R-studio and run Seurat there. -- I learned how to use the Seurat tools in Chipster and what all the steps really mean. I learned to check the results after every step to adjust the next steps parameters and to test different PCA plotting tools. I also learned how to find different genes in the clusters and how to visualize them. I never got this far using the R-pipeline. " -Pinja, course participant & PhD student from University of Helsinki
After this course you should be able to:
- use the Seurat tools available in Chipster to undertake basic analysis of single cell RNA-seq data
- name and discuss the different steps of single cell RNA-seq data analysis
- understand the advantages and limitations of single cell RNA-seq data analysis in general and in Chipster
Keywords: Chipster, Seurat, single cell sequencing, RNA-seq, clustering, aligning cells, cluster markers
Links to material
The relevant material is linked in each course section. Here are some quick links:
Each section of this course contains lecture videos, hands-on exercises and questions/tasks. The tasks can be used to confirm that you have reached the learning goals. You can use the Q&A Forum below to ask questions regarding the course topics or the exercises. Once you have finished all the tasks, you can download a course certificate with a unique course identifier. You can follow your progress with the progress bar on the right. The estimated time to complete the course is 2-3 days. In the certificate we recommend granting 1 credit (ECTS) for the course. In practical matters, please contact event-support (at) csc.fi, and in content related questions, chipster (at) csc.fi.