name: seurat-single-cell-analyzer description: Seurat single-cell analysis skill for clustering, annotation, and trajectory analysis allowed-tools:

• Read
• Write
• Glob
• Grep
• Edit
• WebFetch
• WebSearch
• Bash metadata: version: "1.0" category: bioinformatics tags:
  • transcriptomics
  • single-cell
  • clustering
  • scrnaseq

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)