Inputs and data prep
Prepare compound-target annotations, gene signatures, and pathway sets for frogs pathway analysis.
You provide compound-target annotations, gene expression signatures, and the pathway sets you want scored. Keeping identifiers consistent across targets, signatures, and pathways is what most affects the result — mismatched identifier types are the main cause of dropped rows and partial analyses.
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.
Webapp input methods
The .bloom* webapp provides a comprehensive interface for frogs pathway analysis.
Webapp parameters
Required file inputs
| Parameter | Description | Helper Text |
|---|---|---|
| Compound List File | File path listing compounds for cross-validation | --cpdlist_file |
| Target File | File path for compound target annotations | --target_file |
| Signature File | L1000 gene signatures file path | --sig_file |
| GO-trained Gene Embeddings | Path to GO-trained gene embeddings | --emb_go |
| ARCHS4-trained Gene Embeddings | Path to ARCHS4-trained gene embeddings | --emb_archs4 |
| Output Directory | Directory to save predicted target ranking lists | --outdir |
| Model Directory | Directory to save trained models | --modeldir |
Perturbagen type selection
| Option | Description |
|---|---|
| shRNA | Short hairpin RNA knockdown (default) |
| cDNA | Complementary DNA overexpression |
Training parameters
| Parameter | Range | Default | Description |
|---|---|---|---|
| Number of Epochs | 1+ | 100 | Training iterations |
| Number of Processes | 1-16 | 1 | Parallel processes (--nproc) |
Logging options
- Enable detailed logging to file: Toggle for verbose output
Personalized settings
- Use Personalized Settings: Toggle for project-specific configuration from Supabase
Submit button
- Label: "Start FRoGS Analysis"
- Disabled when: Any required field (compound list, target, signature, embeddings, directories) is empty
Required inputs
- Compound list: IDs used throughout your workspace; include any aliases if multiple systems are used.
- Target annotations: Mappings from compounds to targets (genes/proteins). Ensure consistent identifier types (e.g., HGNC symbols).
- Gene signatures: Expression signatures or embeddings aligned to the same identifiers; typically GO/ARCHS4-style vectors or ranked gene lists.
- Pathway set: Choose from provided sets (e.g., GO/KEGG) or upload a custom list of pathways/terms with member genes.
Optional inputs
- Weights per compound: If some compounds are controls or should be down-weighted.
- Pathway filters: Include/exclude lists to focus on relevant biology.
- Metadata: Cohort labels or experiment IDs to keep outputs traceable.
Formatting tips
- Keep identifiers consistent across targets, signatures, and pathways (e.g., all HGNC or all Ensembl).
- Remove duplicates before upload; frogs will drop exact duplicates but warns on conflicts.
- For ranked gene lists, include directionality if available; for embeddings, confirm dimension compatibility with the workspace.
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