tooluniverse-rnaseq-deseq2
RNA-seq differential expression analysis with DESeq2, edgeR, and limma-voom — DEG lists, fold changes, dispersion estimation, design formulas including covariates, multi-condition contrasts, and Venn-set operations across groups. Routes across DESeq2 (default), edgeR (QL-F / exact test for small replicate counts), and limma-voom (large n / complex designs). Use when you have a count matrix + metadata, want to find DEGs, or need dispersion/PCA/clustering analysis. Includes RULE ZERO precedence (read executed.ipynb if present).
72
90%
Does it follow best practices?
Run evals on this skill
Adds up to 20 points to the overall score
View guide
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
The required runtime workflow ingests outsider-authored free text via loaded data/metadata CSV files (e.g., user-provided counts/metadata and gene annotation tables), where arbitrary string fields (such as gene names, celltype labels, and metadata categories) are read at runtime and used to drive analysis logic and outputs.
- Repository
- mims-harvard/ToolUniverse
- Commit
089eb8e
- Audited
- Security analysis
Is this your skill?
If you maintain this skill, you can claim it as your own. Once claimed, you can manage eval scenarios, bundle related skills, attach documentation or rules, and ensure cross-agent compatibility.