Skill Claude CodeCodex
Determine cell type composition at each spatial location through deconvolution or annotation. Use when user wants to know what cell types exist, their proportions, or where specific cells are located. Triggers: "cell type composition", "deconvolution", "what cells are here", "cell type proportions", "estimate cell…
Skill Claude CodeCodex
Understand cellular differentiation, state transitions, and dynamic processes through trajectory and velocity analysis. Use when user wants to study development, differentiation, cell fate decisions, or temporal dynamics. Triggers: "trajectory", "pseudotime", "RNA velocity", "differentiation", "cell fate", "how do…
Skill Claude CodeCodex
Analyze cell-cell communication patterns and ligand-receptor interactions in spatial context. Use when user wants to understand how cells communicate, signaling pathways, or intercellular interactions. Triggers: "cell communication", "ligand receptor", "cell-cell interaction", "signaling", "how do cells talk"…
Skill Claude CodeCodex
Find differentially expressed genes between conditions, regions, or cell types. Use when user wants to compare gene expression, find markers, or identify condition-specific changes. Triggers: "differential expression", "DEG", "marker genes", "compare conditions", "what genes differ", "find markers", "condition…
Skill Claude CodeCodex
Understand the biological meaning of gene sets through pathway and functional enrichment analysis. Use when user has gene lists (DEGs, markers, SVGs) and wants to know what pathways or functions they represent. Triggers: "pathway analysis", "enrichment", "GSEA", "GO terms", "what pathways", "biological function"…
Skill Claude CodeCodex
Generate publication-quality figures following journal standards for Nature, Cell, and other high-impact journals. Use when user wants to create figures for papers, presentations, or reports with professional formatting. Triggers: "publication figure", "paper figure", "Nature style", "journal figure", "export for…
Skill Claude CodeCodex
Perform complete spatial transcriptomics analysis workflow to understand tissue architecture. Use when user wants to analyze spatial data from Visium, Xenium, MERFISH, Slide-seq, or other platforms. Triggers: "analyze spatial data", "what's the tissue structure", "spatial transcriptomics analysis", "load and analyze"…
Skill Claude CodeCodex
Identify genes and features with significant spatial patterns and organization. Use when user wants to find spatially variable genes, spatial autocorrelation, or spatial clustering patterns. Triggers: "spatially variable genes", "spatial pattern", "Moran's I", "spatial autocorrelation", "which genes vary spatially"…
Skill Claude CodeCodex
Diagnose and resolve common issues in spatial transcriptomics analysis. Use when analysis fails, produces unexpected results, or user encounters errors. Triggers: "error", "failed", "not working", "issue", "problem", "help", "unexpected result", "debug", "fix", "wrong output".
MCP server Claude CodeCodexCursor +2
ChatSpatial: Natural language-driven spatial transcriptomics analysis via Model Context Protocol (MCP) integration. Runs locally from the chatspatial Python package.
Instructions file
Chinese-language project instructions that tell an AI coding assistant to review software with a Linux-kernel-style focus on simplicity, practical design, and compatibility. They also define the required communication style and request-confirmation process.