Downstream Analysis

[KevinMLanderos]

• Network plot for clone_network.csv
• Overlap analysis across samples

Details for sample analysis:

• Alluvial plot showing V(D)J gene usage across time

Details for overlap analysis:

• Using cluster_member_details.csv, group TCR clusters with similar functionality
  Compare shared TCR groups across pairs of patients:
• Venn diagram showing shared and unique clones pre-/post-treatment
• Venn diagram showing shared and unique clones responder vs non-responder

Details for sharing analysis (GLIPH2) -KM:

• pre-/post-treatment
• responder vs non-responder
• Changes in GLIPH2 specificity groups over time
• Highlight significantly expanded GLIPH2 specificity groups
• Waterfall/barplot showing changes (delta) in clone size of the most relevant clones (most expanded before/during/after treatment)