SCMCP scRNA-Seq Server

Example Use Cases

• 1

  Load, save, and inspect single-cell RNA‑seq datasets using natural-language commands.

• 2

  Run preprocessing and analysis pipelines (filtering, normalization, HVG selection, PCA, neighbors, clustering, differential expression) programmatically.

• 3

  Generate common scRNA‑seq visualizations (violin plots, heatmaps, dotplots) and perform cell–cell communication analyses.

Description

SCMCP exposes scRNA-Seq workflows (IO, preprocessing, analysis tools, and plotting) through an MCP interface so users and agents can run scanpy-like operations using natural language. It supports reading/writing data, filtering/QC, normalization, scaling, highly-variable gene selection, PCA, neighbors, clustering, differential expression, and common visualizations (violin, heatmap, dotplot), plus cell–cell communication analysis. It can be run locally or remotely and integrated into AI clients, plugins, and agent frameworks. Note: this repository is marked as no longer maintained and the README points to SCMCPHub for the latest version.