Day 3

“Hang in there. We’re almost there.” — Free Willy (1993)

Before Session

NoteDay 3 Pre-baked Material

Locations

Prebaked from Day 2:

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

Data:

/ourdisk/hpc/iicomicswshp/dont_archive/omics_workshop_2025/day3/data

Scripts:

/ourdisk/hpc/iicomicswshp/dont_archive/omics_workshop_2025/day3/scripts

SCP Reminder

Prebaked from Day 2:

If you have this from Day 2 you do not need to download again

scp -r OSCER_USERNAME@sooner.oscer.ou.edu:'/ourdisk/hpc/iicomicswshp/dont_archive/omics_workshop_2025/day2/data/prebaked' LOCAL_PATH

Data:

scp -r OSCER_USERNAME@sooner.oscer.ou.edu:'/ourdisk/hpc/iicomicswshp/dont_archive/omics_workshop_2025/day3/data' LOCAL_PATH

Scripts:

scp -r OSCER_USERNAME@sooner.oscer.ou.edu:'/ourdisk/hpc/iicomicswshp/dont_archive/omics_workshop_2025/day3/scripts' LOCAL_PATH

• Pre-lecture Reading Link for Day 3

Session Objectives

• Determining the root using Cytotrace
• Pseudotime analysis using Monocle3
• Cell-cell communication using CellChat
• Gene set enrichment analysis (GSEA) using clusterProfiler
• Pathway/transcription factor inference using decoupleR

Session Materials

• Morning Slides by Kurt Zimmerman and Hua Zhong

• Afternoon Slides by by Kurt Zimmerman and Hua Zhong

End of Workshop Feedback Form

• Single Cell RNA-seq 2025 Workshop Feedback Form