Sprint 19

[cristinaetrv]

Overall goal: Prepare for ASHG + wrap up ancestry, imputation, and papers

Due Nov 7

LLM

• Chainlit UI

• Lightweight Demo to get people see to value at ASHG by 11/7

• Can be pretty canned

• Pull out AD genotypes

Poster

• Add edits from lab meeting
• Print by 10/24

Imputation

• Thread through webapp (processing edge cases like 1 chrom per file)
• Verify chrom X works
• Generate chrom X test set (with random missingness)
• Generate chr19 and chr 20 test sets using snp array manifests, and merged chr 19/20 test set
• Report errors when it fails QC
• Handle output directory cleanup

Ancestry

• Test Austin's method by 10/25
• Generate PMRA and 660 lightly pruned versions (test changes in accuracy)
• Liftover PMRA and 660 models
• Test all new models with test sets (PMRA, 660, and Austin's method)

Fair PCA

• Test on daly genotype dosage matrix (IBD PRS sites) by 11/1

POE

• Finish draft and send to Mike E

Proteomics

• Demo outside of CLI (integrated into front end)

• Need to know inputs and outputs

• Clear end-to-end use case (talk to Eric or Erik about prot use case)

• Imputation

• Remove batch effects

• Remove confounders from dominant networks

• pQTL analysis

• Need to understand how prot is currently directly being used

• Method of moments version of batch correction

• (stretch) Follow Eric Dammer's pipeline @akotlar

• (stretch) Replace Eric Dammer's network analysis with SPPCA and compare @akotlar

Webapp

• Make it possible to download APOE report as TSV through API
• Make it possible to download PRS scores as TSV through API
• Update docker container to handle graceful restarts, using pm2