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string-protein-interaction-analysis-with-omicverse

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

OpenClawNanoClawAnalysisWritingbulk-stringdb-ppi🔬 omics & computational biologysingle-cell & spatial omicshelp

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bulk-stringdb-ppi

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • 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.
  • Import omicverse as ov and call ov.utils.ov_plot_set() (or ov.plot_set()) to match omicverse aesthetics.
  • 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.
  • Build dictionaries mapping genes to types and colours, e.g. `gene_type_dict = dict(zip(gene_list, ['Type1']5 + ['Type2']6.

Source Doc

Excerpt From SKILL.md

Examples

  • "Retrieve STRING interactions for FAA4 and plot the network highlighting two gene classes."
  • "Download the STRING edge table for my Saccharomyces cerevisiae gene panel and colour nodes by module."
  • "Extend the network by adding the top five predicted partners before plotting."

Use cases

  • Use string-protein-interaction-analysis-with-omicverse to prepare publication-quality figures.
  • Apply string-protein-interaction-analysis-with-omicverse when results need clear visual communication.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

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