CASCADE: Agentic In Silico Gene Perturbation Analysis via the Model Context Protocol

CASCADE is a Model Context Protocol (MCP) server for in silico gene perturbation analysis in cancer and immuno-oncology research. It provides 28 tools for simulating gene knockdowns and overexpression using pre-computed regulatory networks and GREmLN model embeddings across 10 immune and epithelial cell types, with LangGraph-based workflow orchestration, parallel batch execution, cross-source evidence synthesis, and 8 integrated data sources. Data license note (added 2026-10-03): This archive includes TCGA ARACNe network files (data/networks/tcga/) converted from the Bioconductor aracne.networks package. These files are not covered by CASCADE's MIT license and remain under their upstream license terms, which permit non-commercial academic research use only. CASCADE version 1.4.2 and later (https://doi.org/10.5281/zenodo.23127366) do not include these files.