StatefulDiscovery

Invoke after experiment-runner completes an investigation's query bundle. Evaluates all claims in current_investigation.json and produces an investigation-level adjudication. Writes claim_scores.json.

Invoke after investigation-decomposition. Runs all queries in an investigation bundle using shared data preparation. Writes code and results.

Invoke after main agent writes L2 assessment. Reads epistemic state (L1/L2), patterns, and investigations to recommend next action. Writes strategy_recommendation.json.

Gene set enrichment analysis (GSEA, Enrichr, over-representation). Invoke when query mentions enrichment, pathway analysis, GO analysis, GSEA, or gene set.

Invoke before running experiments for an investigation. Reads current_investigation.json and task_packet.json, writes current_investigation_requirements.json with shared data preparation and per-query requirements.

Gene ID conversion and annotation. Invoke when you need to map between any gene identifier formats.

Phylogenetic analysis: multiple sequence alignment (MAFFT), tree building (IQ-TREE, FastTree), tree metrics (treeness, branch lengths, patristic distances). Invoke when query involves phylogenetic trees, evolutionary analysis, sequence alignment, treeness, or tree statistics.

Differential expression analysis for RNA-seq count data. Invoke when query mentions DESeq2, differential expression, DE genes, or RNA-seq comparison.

NGS data processing: read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ. Calculate coverage, perform pileup, run samtools/bcftools commands. Invoke when query involves sequencing alignment, variant calling, coverage depth, or read mapping.

Invoke before final output. Validates that all claims have reproducible evidence (code files exist, experiment records complete). Run the bundled Python script.

Single-cell RNA-seq analysis pipeline. Invoke for .h5ad data, QC, normalization, PCA/UMAP, clustering, marker genes, cell type annotation.

Invoke for claims.json final output format reference. Defines the schema for aggregated claims across all investigations.

Invoke before writing experiments.jsonl. Provides the exact JSON structure and required fields for experiment records.

Invoke for investigations.json and current_investigation.json format reference. Defines the schema for claim investigations and query bundles.

Invoke for patterns.json format reference. Defines the schema for tracking unexplained data patterns.

Invoke for epistemic_state.json format reference. Defines the global exploration state schema with L1/L2 uncertainty assessment.

Gene set enrichment analysis (GSEA, Enrichr, over-representation). Invoke when query mentions enrichment, pathway analysis, GO analysis, GSEA, or gene set.

Invoke before final output. Validates that all claims have reproducible evidence (code files exist, experiment records complete). Run the bundled Python script.