string-protein-interaction-analysis-with-omicverse
Help Claude query STRING for protein interactions, build PPI graphs with pyPPI, and render styled network figures for bulk gene lists.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bulk-stringdb-ppi --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# STRING protein interaction analysis with omicverse ## Overview 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`](../../omicverse_guide/docs/Tutorials-bulk/t_network.ipynb), covering species selection, S TRING API queries, and quick visualisation of the resulting network. ## Instructions 1. **Set up libraries** - Import `omicverse as ov` and call `ov.utils.ov_plot_set()` (or `ov.plot_set()`) to match omicverse aesthetics. 2. **Collect gene inputs** - Accept a curated list of gene symbols (`gene_list = [...]`). - Encourage the user to flag priority genes or categories so you can colour-code groups in the plot. 3. **Assign metadata for plotting** - Build dictionaries mapping genes to types and colours, e.g. `gene_type_dict = dict(zip(gene_list, ['Type1']*5 + ['Type2']*6 ))` and `gene_color_dict = {...}`. - Remind users that consistent group labels improve legend readability. 4. **Query STRING interactions** - Call `ov.bulk.string_interaction(gene_list, species_id)` where `species_id` is the NCBI taxonomy ID (e.g. 4932 for yeast). - Inspect the resulting DataFrame for co
- Overview
- Instructions
- Examples
- References
What does the string-protein-interaction-analysis-with-omicverse skill do?
Help Claude query STRING for protein interactions, build PPI graphs with pyPPI, and render styled network figures for bulk gene lists.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bulk-stringdb-ppi --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.