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Get Started Free →Help Claude query STRING for protein interactions, build PPI graphs with pyPPI, and render styled network figures for bulk gene lists.
.claude/skills/string-protein-interaction-analysis-with-omicverse/SKILL.md| Test case | Without → With | Effect | Δ tokens | Δ turns |
|---|---|---|---|---|
| case-04 | ✗→✓ | ▲ Improved | — | — |
| case-17 | ✗→✓ | ▲ Improved | — | — |
| case-13 | ✗→✓ | ▲ Improved | — | — |
| case-06 | ✗→✓ | ▲ Improved | — | — |
| case-01 | ✗→✓ | ▲ Improved | — | — |
Invoke this skill when the user has a list of genes and wants to explore STRING protein–protein interactions via omicverse. The workflow mirrors t_network.ipynb, covering species selection, S TRING API queries, and quick visualisation of the resulting network.
omicverse as ov and call ov.utils.ov_plot_set() (or ov.plot_set()) to match omicverse aesthetics.gene_list = [...]).)) and gene_color_dict = {...}.
ov.bulk.string_interaction(gene_list, species_id) where species_id is the NCBI taxonomy ID (e.g. 4932 for yeast).ppi = ov.bulk.pyPPI(gene=gene_list, gene_type_dict=..., gene_color_dict=..., species=species_id).ppi.interaction_analysis() to fetch and cache STRING edges.ppi.plot_network() to reproduce the notebook figure.ov.utils.plot_network keyword arguments ifthe user requests adjustments.
queries fail.
ppi.interaction_analysis(add_nodes=...) to expand the network.
t_network.ipynbreference.md| Case | Status | Duration (ms) | Turns | Tokens | Tool calls | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Without | With | Δ | Without | With | Δ | Without | With | Δ | Without | With | Δ | ||
case-04 | fail→pass | — | — | — | — | — | — | — | — | — | — | — | — |
case-10 | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
case-14 | pass→pass | — | — | — | — | — | — | — | — | — | — | — | — |
case-17 | fail→pass | — | — | — | — | — | — | — | — | — | — | — | — |
case-13 | fail→pass | — | — | — | — | — | — | — | — | — | — | — | — |
case-22 | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
case-06 | fail→pass | — | — | — | — | — | — | — | — | — | — | — | — |
case-01 | fail→pass | — | — | — | — | — | — | — | — | — | — | — | — |
case-18 | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
case-08 | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
case-11 | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
case-09 | fail→pass | — | — | — | — | — | — | — | — | — | — | — | — |
case-19 | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
case-20 | fail→pass | — | — | — | — | — | — | — | — | — | — | — | — |
case-12 | fail→pass | — | — | — | — | — | — | — | — | — | — | — | — |
case-02 | pass→pass | — | — | — | — | — | — | — | — | — | — | — | — |
case-07 | fail→pass | — | — | — | — | — | — | — | — | — | — | — | — |
case-15 | pass→pass | — | — | — | — | — | — | — | — | — | — | — | — |
case-03 | fail→pass | — | — | — | — | — | — | — | — | — | — | — | — |
case-05 | fail→pass | — | — | — | — | — | — | — | — | — | — | — | — |
case-16 | pass→pass | — | — | — | — | — | — | — | — | — | — | — | — |
case-21 | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
DecimalAI ran this skill against gemini-3.6-flash twice over the same eval suite — once with the skill loaded and once without — and compared the two runs case by case. 22 cases were attempted. The headline lift of +50 percentage points is the difference between those two pass rates over the 22 comparable cases.
The per-case answers from this run were removed by the retention sweep, so the case table below shows the verdicts without the text either arm produced. The counts above were recorded at the time and are unaffected. Answers are now kept for 180 days.
Other measured skills in the registry, with their headline benchmark lift.