Objectives
- Understand and learn the main steps of scRNA-seq data analysis, up to marker gene detection and cell type identification.
- Be able to use the Seurat package on a small test dataset, from count matrices to clustering and cluster annotation.
- Understand the basics of the analysis in order to apply them to one’s own dataset.
Course Content
I. Introduction
- Single-cell RNA sequencing
- From raw sequencing data to count matrices
- Software tools
II. Preprocessing of the expression matrix (Theory and Practice)
- Quality control
- Normalization
- Dimensionality reduction (HVG, PCA, UMAP)
- Detection of expression biases
III. Annotation (Theory and Practice)
- Clustering
- Marker genes
- Cell type identification
- Analysis of marker gene lists with the R package ClusterProfiler
IV. Practical Workshop “Bring your own data”
- Semi-autonomous execution of primary analysis on learners’ own data
Prerequisites
- Good knowledge of R or having completed the training “Bioanalysis Training: Introduction to the R Programming Language.”
- Have your own data or data of interest collected from public databases (cellXgene, Single Cell Portal, …).
Duration
- 2,5 days / 18 hours
Fees
- Academics Nantes Université: 590 euros
- Others academics: 680 euros
- Private sector: 1630 euros
Teaching Methods
- Combination of lectures and practical exercises.
Instructors
- Bioinformatics engineers from BiRD
Validation
Certificate of attendance provided to each participant on request
Registration
Register Here (except for PhD students - via Amethis)
