SingleCellRNAseqWorkshop2024

This is the repository for the Workshop on single-cell RNA-seq data analysis, organized at the IMBEI by the Bioinformatics group.

Content of this repository:

• Introductory lecture
• Practical session(s)
• Link to exemplary dataset
• Spotlight presentations on specific aspects of the analysis

How to use this?

• Clone this repository/Download this locally
• Start RStudio by clicking on the .Rproj file contained in the top level of the directory
• Navigate the material from inside the IDE
• Get your hands dirty!

Schedule

Day1

• 9:00-9:30: Welcome and introduction round

  • Setup and installation check

• 9:30-12:00: Single-cell RNA-seq lecture (break in between)

  • 101 on RMarkdown, got data?

• 12:00-13:00: Lunch break

• 13:00-17:00: Practical session

  • Retrieval of counts data via seafile
  • Quality control and filtering
    • Spotlight presentation
  • Data integration
    • Spotlight presentation
  • iSEE the data
  • Q&As from the attendees
  • Homework: think, what would you ask to this dataset?

Day2

• 9:00-9:30: Recap on the content of day1
• 9:30-10:00: Lecture on data exploration and visualization
• 10:00-12:00: Practical session
  • Cell type annotation
    • Spotlight presentation
  • Differential analyses - DA&DE + iSEE
• 12:00-13:00: Lunch break
• 13:30-16:00: Pratical session
  • Splitting up the monolyth: QC, integration, differential
  • Focus on some topics of interest touched upon during the workshop
  • Advanced Q&As from the attendees
  • Feedback round & posting link to feedback form

Feedback form (Feb 2024): https://forms.gle/z6ssFmuLW56uTPYt6

License

CC BY-SA 4.0