tooluniverse-single-cell
Single-cell RNA-seq analysis with scanpy/anndata — h5ad data loading, scRNA-seq quality control and QC gating (n_genes_by_counts, total_counts, mitochondrial percent / pct_counts_mt, pct_counts_ribo, doublet detection with Scrublet/scDblFinder, ambient RNA / SoupX awareness, empty-droplet filtering, MAD-based thresholds), normalization, dimensionality reduction (PCA, UMAP, t-SNE), clustering (Leiden, Louvain), marker gene identification, cell-type annotation, pseudotime/trajectory analysis. Use for any scRNA-seq workflow, including deciding which cells to filter, flag, or investigate before downstream analysis.
72
88%
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Low
Low-risk findings worth noting
Low
Low-risk findings.
1 low severity finding. Worth noting, but not necessarily harmful.
W011: Third-party content exposure detected (indirect prompt injection risk).
What this means
The skill exposes the agent to untrusted, user-generated content from public third-party sources, creating a risk of indirect prompt injection. This includes browsing arbitrary URLs, reading social media posts or forum comments, and analyzing content from unknown websites.
Why it was flagged
In `SKILL.md` the workflow ingests user-selected content via ToolUniverse tool execution (e.g., `tu.run_tool("OmniPath_get_ligand_receptor_interactions", ...)` in `references/cell_communication.md`), where outsider-provided free text (such as `proteins`/`databases` parameters derived from the user question) can flow into the runtime path that reads and returns database text.
- Repository
- mims-harvard/ToolUniverse
- Commit
089eb8e
- Audited
- Security analysis
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