scanpy
Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, visualization, and converting R-friendly single-cell formats such as Seurat or SingleCellExperiment RDS files into h5ad for Scanpy. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.
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Low
Low-risk findings worth noting
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
The workflow ingests user-supplied cell-type mapping JSON files via `annotate.py` and gene signature JSON files via `score_genes.py`, both of which parse outsider-authored free text into agent configuration structures without prior selection.
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- K-Dense-AI/scientific-agent-skills
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49c6e97
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- Security analysis
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