Background lists for GSEA, analysis direction, overlap target number by polrus · Pull Request #27 · opentargets/pathways-api

polrus · 2026-01-27T15:55:37Z

Changes

Background gene lists: Auto-generate per-GMT background gene lists at startup
Background gene merging: Merge library background genes (with zero scores) into input for more accurate GSEA results
Analysis direction: New analysis_direction parameter (one_sided_positive, one_sided_negative, two_sided)
Input overlap stats: Response includes input_overlap showing input/library gene overlap

…is direction to GSEA endpoint

…ed code

polrus added 10 commits January 27, 2026 15:35

fix: gsea.py json format

a050ce0

fix: gsea - JSON-safe values

8d0e796

feat: generate per-GMT background gene lists and run on startup

2cca721

feat(gsea): merge library background genes into input with zero scores

3f819b4

fix(ui): update routing and API proxy

295a2cf

fix: handle NaN values for JSON serialization

5111d50

feat(logging): enhance logging for router registration and add analys…

fea106b

…is direction to GSEA endpoint

refactor(gsea): rename missing_stats to input_overlap

5a5d95c

refactor(router): simplify router registration

1c7e853

refactor(router): clean up temporary file handling and remove comment…

6447fec

…ed code

polrus requested a review from carcruz January 27, 2026 15:55

carcruz approved these changes Feb 4, 2026

View reviewed changes

carcruz merged commit 0c8b995 into main Feb 4, 2026
1 check passed

carcruz deleted the feat-gmt-background-lists-backend-only branch February 4, 2026 11:01

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