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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

  1. Introduction of the Companions and Instructors (10 min)
  2. Presentation of the IOC general workflow (Scheme) (15 min)
  3. Work Program of the week 0
    • Import data
    • Create a genome annotation with Biomart

Week 1 - 30/04/2024

  1. Questions on Week 0 [Visioconference]
  2. Preprocessing
  3. How to filter out low quality barcodes
  4. Normalize data
  5. Identify Highly Variable Genes (HVG)
  6. Program of Week 1
    • Exercices with RStudio and R scripting

Week 2 - 08/05/2024

  1. Questions on Week 1 [Visioconference]
  2. Reduction of dimensionality (PCA & UMAP)
  3. Inspect PCA
  4. Program of Week 2
    • Exercices with RStudio and R scripting

Week 3 - 15/05/2024

  1. Questions on Week 2 [Visioconference]
  2. Clustering barcodes
  3. Choosing a meaningful partition
  4. Program of Week 3
    • Exercices with RStudio and R scripting

Week 4 - 22/05/2024

  1. Questions on Week 3 [Visioconference]
  2. Visualization of gene markers for each cluster
  3. Differential Gene Expression
  4. Program of Week 4
    • Exercices with RStudio and R scripting

Week 5 - 29/05/2024

  1. Questions on Week 4 [Visioconference]
  2. Over-representation Analysis with ClusterProfiler
  3. Program of Week 5
    • Exercices with RStudio and R scripting

Week 6 - 05/06/2024

  1. Questions on Week 5 [Visioconference]
  2. Gene Set Enrichment Analysis with ClusterProfiler
  3. Program of Week 6
    • Exercices with RStudio and R scripting

Week 7 - 12/06/2024

  1. Questions on Week 6 [Visioconference]
  2. Assign cell type identity to clusters
  3. Visualizations
  4. 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)

  1. Questions on Week 7 (30 minutes max) [Visioconference]
  2. 20 min presentations by the attendees