Schedule
In this Interactive Online Companionship which will be held in April 2024. We will train to use the R programming language for single cell RNAseq data analysis.
Week 0 - 24/04/2024¶
- Introduction of the Companions and Instructors (10 min)
- Presentation of the IOC general workflow (Scheme) (15 min)
- Work Program of the week 0
- Import data
- Create a genome annotation with Biomart
Week 1 - 30/04/2024¶
- Questions on Week 0 [Visioconference]
- Preprocessing
- How to filter out low quality barcodes
- Normalize data
- Identify Highly Variable Genes (HVG)
- Program of Week 1
- Exercices with RStudio and R scripting
Week 2 - 08/05/2024¶
- Questions on Week 1 [Visioconference]
- Reduction of dimensionality (PCA & UMAP)
- Inspect PCA
- Program of Week 2
- Exercices with RStudio and R scripting
Week 3 - 15/05/2024¶
- Questions on Week 2 [Visioconference]
- Clustering barcodes
- Choosing a meaningful partition
- Program of Week 3
- Exercices with RStudio and R scripting
Week 4 - 22/05/2024¶
- Questions on Week 3 [Visioconference]
- Visualization of gene markers for each cluster
- Differential Gene Expression
- Program of Week 4
- Exercices with RStudio and R scripting
Week 5 - 29/05/2024¶
- Questions on Week 4 [Visioconference]
- Over-representation Analysis with ClusterProfiler
- Program of Week 5
- Exercices with RStudio and R scripting
Week 6 - 05/06/2024¶
- Questions on Week 5 [Visioconference]
- Gene Set Enrichment Analysis with ClusterProfiler
- Program of Week 6
- Exercices with RStudio and R scripting
Week 7 - 12/06/2024¶
- Questions on Week 6 [Visioconference]
- Assign cell type identity to clusters
- Visualizations
- Program of Week 7
- Exercices with RStudio and R scripting
- Small project with a specific objective
Week 8 - Presentations of the analyses by the companions (september 2024)¶
- Questions on Week 7 (30 minutes max) [Visioconference]
- 20 min presentations by the attendees