Analysis parameters
The pathway set, scoring mode and coverage thresholds that FRoGS scoring used. FRoGS is deprecated, its backend is offline, and it can no longer be run.
These settings control how frogs scores compounds against pathways — the pathway set, how compound-target links and signatures are weighted, and the coverage and completeness thresholds. The scoring mode and coverage thresholds are what most affect which compounds stay in the analysis and how pathways rank.
Not available in chat
FRoGS is deprecated on the platform and its Modal backend has been taken offline — it is not registered with the orchestrator, so chat cannot call it. Existing FRoGS job results should be treated as unverified: a still-registered legacy form of the tool faked its results, returning mock predictions as SUCCESS regardless of input.
Core settings
- Pathway set: Choose the ontology or custom list to score against.
- Scoring mode: Select how compound-target links are weighted (e.g., equal weights vs. target-aware weights).
- Signature weighting: Optionally weight signatures by quality/confidence if your dataset supports it.
Thresholds
- Minimum target coverage: Require a minimum number of mapped targets per compound to keep it in the analysis.
- Signature completeness: Set a tolerance for missing genes/features; signatures below the threshold are dropped with a warning.
- P-value / FDR cutoffs: Configure significance thresholds for pathway calls when available in your workspace.
Performance and batching
- Large pathway sets or signature matrices may be batched; keep batch size defaults unless you see timeouts.
- If jobs run long, reduce pathway scope or tighten completeness thresholds.
Recommendations
- Start with the default pathway set and moderate thresholds, then tighten as you refine hypotheses.
- Use the same pathway set across related runs to make comparisons consistent.
- When exploring new datasets, enable verbose validation so you can inspect any dropped inputs.
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