bystrogenomics / bystro

Natural Language Search and Analysis of High Dimensional Genomic Data
Mozilla Public License 2.0
44 stars 14 forks source link

Sprint 14 Task List #536

Open cristinaetrv opened 4 months ago

cristinaetrv commented 4 months ago

Proteomics:

PRS-CS:

PRS LD Clumping + Thresholding v2:

Ancestry V2:

Ancestry V2 (post subject mapping integration):

POE module:

ML library:

Backlog for Sprint 15

akotlar commented 3 months ago

2024-07-12 Sync Meeting

PRS-CS

Imputation in Python is done, 75% complete Rust module delivered to @akotlar genotype_imputation.rs.zip. Now @akotlar to link to Python through Maturin/PyO3 and make sure it works. Will work with @austinTalbot7241993

We can already take covariates, just need to wrap it into Python and feed through UI which is on @akotlar - will be next sprint

POE module

1000x faster than POIROT, so we don't need JIT. We will pre-compute permutations for specific MAFs. Do the permutation test once, to get the p-values under null, and the actual effect estimates are also 1000x faster than POIROT, are very quick, so don't add much to runtime overall.

POE draft done ParentofOriginEffect.pdf

Will notify Mike today.

Scheduler (API)

Done this weekend

akotlar commented 3 months ago

2024-07-17

Alex

Finishing up somascan join to annotation + threading through covariates

Ilha

Finishing covariance hypothesis testing

Austin

This week is finishing draft (@akotlar needs to go through it by 2024-07-19). Goal is to get it posted by end of next week.

Cristina

Checking over on lifted over sumstats (hg19) file, may not be compressed. Finishing reading last year's grant and looking up resources Thomas.