Day 2

“Just keep swimming.” — Finding Nemo (2003)

Before Session

NoteDay 2 Pre-baked Material Location

/ourdisk/hpc/iicomicswshp/dont_archive/omics_workshop_2025/day2/data/

NoteDay 2 Scripts Location

/ourdisk/hpc/iicomicswshp/dont_archive/omics_workshop_2025/day2/scripts/

• Pre-lecture Reading Link for Day 2

Session Objectives

• Understanding how the R package Seurat works as the core framework for:
  • Data quality checking and filtering
  • Integration across samples
  • Visualization
  • Clustering of cells
  • Annotating cell using a custom atlas
  • Sub-clustering of specific cell types

Session Materials

• Morning Slides by Lindsay Hayes

• Afternoon Slides by Lindsay Hayes

Breakout Session Guides

• Session 1 - Seurat Creation to Normalization

  • Session 1 Answers

• Session 2 - Dimension Reduction

  • Session 2 Answers

• Session 3 - Integration

  • Session 3 Answers

• Session 4 - Cluster Markers

  • Session 4 Answers

• Session 5 - Annotation

  • Session 5 Answers

• Session 6 - Abundance

  • Session 6 Answers

• Session 7 - Sub-Clustering

  • Session 7 Answers