Outputs and interpretation

frogs returns ranked pathways with enrichment scores and compound-to-pathway contribution metrics, plus a report of any dropped inputs. Use these to prioritize follow-up candidates for wet-lab validation, generate mechanism-of-action hypotheses, and compare runs across cohorts.

What you receive

• Pathway rankings: Scores and significance measures per pathway, with enrichment metrics when available.
• Compound-to-pathway links: Contribution scores showing which compounds drive each pathway call.
• Dropped inputs report: Any signatures or compounds excluded during validation with reasons.
• Downloads: CSV/JSON exports of pathway tables and compound-pathway scores.

How to interpret

• High pathway scores indicate stronger alignment between signatures/targets and the pathway gene set; verify significance cutoffs before acting.
• Use compound contribution scores to pick follow-up candidates for wet lab validation.
• Compare runs using the same pathway set to assess consistency across cohorts or parameter changes.

Downstream actions

• Share pathway summaries with biology teams for hypothesis generation.
• Export compound-pathway tables for visualization, clustering, or cross-tool comparisons.
• Feed prioritized compounds into downstream validation (docking, wet lab assays, or safety models).

Troubleshooting

• Empty or sparse outputs: Check the dropped inputs report for missing targets or malformed signatures, then re-run after fixing.
• No significant pathways: Loosen significance thresholds slightly or broaden the pathway set to increase coverage.
• Long runtimes: Reduce pathway set size or batch size, or limit to high-confidence signatures.

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