The Agent Skills Directory

[COMMAND_EXECUTION]: The skill invokes the MaxQuantCmd.exe binary locally to perform proteomics database searches. This is a primary function of the tool and is executed within the user's local environment.
[EXTERNAL_DOWNLOADS]: The skill references the official maxquant.org website for software downloads and utilizes standard Python package managers (pip) to install well-known libraries such as pandas and scipy.
[SAFE]: Network interactions are limited to well-known bioinformatics platforms, specifically string-db.org and Enrichr (via gseapy), for the purpose of protein pathway enrichment. No sensitive data is transmitted to these services.
[SAFE]: The skill ingests data from local proteinGroups.txt files. While this represents a data ingestion surface, the processing involves statistical analysis and visualization rather than code execution or instruction processing. Ingestion points: proteinGroups.txt is read from the local file system using pandas. Boundary markers: Standard CSV/TSV delimiters are used; no specific security boundaries for text instructions are present. Capability inventory: Local subprocess execution of the MaxQuant search engine. Sanitization: Data is parsed into structured pandas DataFrames for numerical computation.

maxquant-proteomics