# Seurat Single Cell Analyzer

> Seurat single-cell analysis skill for clustering, annotation, and trajectory analysis

- Skill: `a5c-ai/seurat-single-cell-analyzer` (Agent Skill)
- Install (CLI): `npx skillmds@latest add a5c-ai/seurat-single-cell-analyzer`
- Raw SKILL.md: https://api.skillmd.com/api/skills/a5c-ai/seurat-single-cell-analyzer/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: a5c-ai (https://skillmd.com/u/a5c-ai)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/a5c-ai/seurat-single-cell-analyzer

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# Seurat Single-Cell Analyzer Skill

## Purpose
Enable Seurat single-cell analysis for clustering, annotation, and trajectory analysis of scRNA-seq data.

## Capabilities
- Quality filtering and normalization
- Dimensionality reduction (PCA, UMAP)
- Graph-based clustering
- Marker gene identification
- Cell type annotation
- Integration across datasets
- Trajectory inference

## Usage Guidelines
- Apply quality filters appropriate for experiment
- Normalize data before dimensionality reduction
- Select clustering resolution based on biology
- Identify markers for cluster annotation
- Integrate datasets to remove batch effects
- Document analysis parameters

## Dependencies
- Seurat
- Scanpy
- CellRanger

## Process Integration
- Single-Cell RNA-seq Analysis (scrnaseq-analysis)
- Spatial Transcriptomics Analysis (spatial-transcriptomics)