scrna-celltype-annotation

What problem does it solve?

This Skill automates the process of annotating single-cell RNA sequencing (scRNA-seq) clusters with precise cell types and provides robust literature-based evidence, streamlining the analysis and reporting workflow.

Core Features & Use Cases

• Automated Cell Type Annotation: Assigns both major and minor cell type labels to clusters based on differential gene expression (DGE) markers.
• Literature-Based Evidence: Retrieves and cites relevant scientific literature (e.g., from PubMed, OpenAlex) to support each annotation.
• R Recode Code Generation: Produces R code for easy integration of annotations back into Seurat objects.
• Structured Markdown Reports: Generates comprehensive reports detailing annotations, supporting evidence, and R code.
• Use Case: After running differential expression analysis on your scRNA-seq data, use this Skill to automatically identify the cell types within each cluster and generate a report with citations for your publication.

Quick Start

Use the scrna-celltype-annotation skill to annotate cell clusters from the provided Seurat DGE results CSV file and generate a markdown report with R recode code.