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CLI Reference

Commands

panel score <GENES...>

Score proteins by multi-criteria ranking (demand + feasibility).

panel score TNF IL6 CXCL10 GDF15
panel score TNF IL6 --weights demand=3,uniqueness=2
panel score TNF IL6 --format json --output scores.json

Options: --weights, --format (table|json|csv), --output

panel propose <GENES...>

Generate an optimized panel from candidates.

panel propose TNF IL6 GDF15 CXCL10 VEGFA CCL2 --size 5
panel propose ... --exclude TNF,IL6
panel propose ... --pareto
panel propose ... --max-per-pathway 3

Options: --size, --exclude, --pareto, --max-per-pathway, --format, --output

panel demo [DISEASE]

Quick panel proposal from disease-specific seed proteins.

panel demo --list           # show categories
panel demo alzheimer        # score 10 seeds, propose top 5
panel demo cardio --size 8  # larger panel

Options: --list, --size, --format

panel enrich <GENES...>

Full protein context from all sources.

panel enrich TNF IL6 GDF15 --format json

Returns: gene_name, nih_grants, pub_growth_3yr, trials_active, blood_detectable, competitors_measuring, diseases, pathways.

panel compare <GENES...>

Side-by-side comparison against competitor panels.

panel compare TNF IL6 GDF15 CXCL10 VEGFA
panel compare TNF IL6 --competitor alamar

panel gaps

Proteins competitors have that Olink doesn't.

panel gaps --top 20
panel gaps --competitor nomic --format json

panel pathways

Pathways with low Olink coverage.

panel pathways --min-members 10 --top 15
panel pathways --include-pathogen

panel backtest <GENES...>

Publication coverage validation.

panel backtest TNF IL6 GDF15 CXCL10 VEGFA
panel backtest TNF IL6 GDF15 --per-protein --years 5

panel cooccurrence <GENES...>

Publication co-mention clustering.

panel cooccurrence TNF IL6 CCL2 GDF15 VEGFA IL1B --cluster

panel xreactivity <GENES...>

Cross-reactivity risk check (InterPro family overlap).

panel xreactivity TNF IL6 IL1B CXCL10 CCL2

panel tui

Launch interactive arrow-key TUI.

panel tui
# or equivalently:
uv run 00panel