The Agent Skills Directory

[PRIVILEGE_ESCALATION]: The references/r_interop.md guide provides instructions for installing system-level dependencies for R interoperability using sudo apt-get or sudo dnf. While necessary for setting up a bioinformatics environment on Linux, these commands require elevated privileges to manage system packages.\n- [UNVERIFIABLE_DEPENDENCIES_AND_REMOTE_CODE_EXECUTION]: The R interoperability instructions in references/r_interop.md include commands to install software from the mojaveazure/seurat-disk GitHub repository. Additionally, the skill's scripts suggest installing Python packages like harmonypy, bbknn, and scikit-image. While these are standard tools in the single-cell analysis community, they originate from various third-party maintainers.\n- [DYNAMIC_EXECUTION]: The skill facilitates data format conversion by generating and executing R scripts (e.g., convert_rds_to_h5ad.R) to bridge the gap between R-native single-cell objects and Python's AnnData format.\n- [INDIRECT_PROMPT_INJECTION]: The skill processes complex external data files (.h5ad, .csv, .rds, and 10X Genomics formats). This represents a data ingestion surface where maliciously crafted data files could theoretically exploit vulnerabilities in the underlying scientific computing libraries like Scanpy, AnnData, or Pandas.

scanpy