Workflow Examples

This section contains complete analysis workflows demonstrating how to use ChatSpatial for real-world spatial transcriptomics research.

Available Workflows

Case Studies

Mouse Brain Visium Analysis

Complete workflow for analyzing mouse brain tissue using 10x Visium technology.

What this workflow covers:

  • Loading and preprocessing Visium data
  • Spatial domain identification
  • Cell type annotation
  • Visualization techniques
  • Biological interpretation

Dataset: Adult mouse brain coronal section
Technology: 10x Visium
Time: ~2 hours
Level: Beginner to Intermediate

Workflow Categories

By Analysis Type

  • Basic Workflows - Standard preprocessing and visualization
  • Cell Type Analysis - Annotation and validation workflows
  • Spatial Statistics - Pattern analysis and statistical testing
  • Multi-sample Integration - Batch correction and comparison
  • Advanced Methods - Machine learning and trajectory analysis

By Tissue Type

  • Brain Tissue - Neural development and function
  • Cancer Samples - Tumor microenvironment analysis
  • Development - Embryonic and organoid studies
  • Pathology - Disease progression studies

By Technology

  • 10x Visium - Standard spatial transcriptomics
  • MERFISH - High-resolution spatial analysis
  • Slide-seq - Bead-based approaches
  • Integration - Multi-modal analysis

How to Use These Workflows

  1. Choose a workflow that matches your research question
  2. Download sample data or use your own similar dataset
  3. Follow the conversation examples - they show real ChatSpatial interactions
  4. Adapt the analysis to your specific research needs
  5. Modify parameters based on your data characteristics

Contributing Workflows

We welcome community contributions of analysis workflows. To add your workflow:

  1. Create a detailed analysis document
  2. Include conversation examples
  3. Provide sample data or clear data requirements
  4. Add biological interpretation and insights
  5. Submit via GitHub pull request

Workflow Template

When creating new workflows, please include:

  • Overview - Research question and approach
  • Data Requirements - Format, size, and characteristics needed
  • Step-by-step Analysis - Complete ChatSpatial conversation flow
  • Expected Results - What outputs to expect
  • Biological Interpretation - How to understand the results
  • Troubleshooting - Common issues and solutions
  • Extensions - How to build on this analysis

Getting Help

For questions about specific workflows, please check the individual workflow documentation or open a discussion on GitHub.

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