The Agent Skills Directory

[DYNAMIC_EXECUTION]: The documentation in 'references/workflow_guide.md' explicitly demonstrates and guides users to use the 'pickle' module ('pickle.load') to restore count matrices, metadata, and AnnData objects from files such as 'counts.pkl', 'metadata.pkl', and 'dds_result.pkl'. Python's pickle serialization mechanism is inherently unsafe for processing files from unvalidated or external sources, as it can be leveraged to execute arbitrary code during deserialization. Remediation requires advising the use of safer serialization alternatives like native CSV/TSV, Parquet, or AnnData's built-in H5AD file format options ('read_h5ad'), which do not allow arbitrary code execution.

pydeseq2