monarch-initiative
@monarch-initiative Organization
Public Skills
run-deep-research
by monarch-initiative
Toolkit for performing deep research on complex topics using multiple AI research providers (OpenAI, Falcon, Perplexity, Consensus). Emphasizes explicit speed vs depth trade-offs.
gene-set-enrichment
by monarch-initiative
Perform gene set enrichment analysis using AI research providers. Analyzes lists of genes to identify biological themes, pathways, and functional associations.
evaluate-enrichment
by monarch-initiative
Use when evaluating a GO enrichment method or a GOA evidence variant (all vs IBA vs IBA+IEA vs no-contributes_to) against the curated benchmark in this repo — the IBA/evidence-ablation eval. Covers building queries.gmt, prepare_go_eval, running genesets-rs, and scoring with the confirmatory/mechanistic split and the recovery_status diagnostics, plus the don't-refit-the-gold guardrail.
curate-geneset
by monarch-initiative
Use when curating or reviewing a GO-term interpretation of a non-GO gene set (MSigDB C8/C2/H, literature disease-activity, or GWAS/CRISPR genetics) for the curation/ gold standard in this repo. Covers grounding in the real membership, OLS term verification, the category / recovery_status / insight axes, evidence, series, the 4-gate validator, and folding the set into the eval.