pydeseq2
Warn
Audited by Gen Agent Trust Hub on Mar 31, 2026
Risk Level: MEDIUMREMOTE_CODE_EXECUTIONEXTERNAL_DOWNLOADSCOMMAND_EXECUTION
Full Analysis
- [REMOTE_CODE_EXECUTION]: The documentation provides examples of using Python's pickle module for data loading, which is a significant security risk as it can facilitate arbitrary code execution during the deserialization process.
- Evidence: Code snippets in references/workflow_guide.md demonstrate loading data matrices using pickle.load().
- Evidence: The api_reference.md documentation suggests saving and loading object states using the picklable AnnData format.
- [EXTERNAL_DOWNLOADS]: The skill requires the installation of several external dependencies from the Python Package Index (PyPI).
- Evidence: SKILL.md lists requirements for pydeseq2, pandas, numpy, scipy, scikit-learn, and anndata.
- [COMMAND_EXECUTION]: The skill includes a standalone script for batch processing genomic data via the command line.
- Evidence: The scripts/run_deseq2_analysis.py file is a complete utility for executing differential expression analysis from a shell environment.
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