Spatial Transcriptomics Analysis Reports
Spatial Reports
A template repository providing analysis workflows for spatial single-cell transcriptomics data across multiple experimental platforms and analytical packages. This project offers researchers standardized pipelines for quality control, clustering, and cell-type annotation.
Key Features
- Multi-Platform Support: Templates for COSMX and Visium[HD] spatial transcriptomics platforms
- Quality Control Pipelines: Comprehensive QC assessment workflows for data validation
- Clustering Workflows: Spatial clustering using Banksy and other established tools
- Cell-Type Annotation: Integration with spacexr for cell-type identification and differential expression
- Reproducible Environment: RStudio Projects with renv package management for dependency control
Technical Stack
Built entirely in R with integration of leading bioinformatics tools:
- Seurat for Visium object handling
- Banksy for spatial clustering analysis
- spacexr for cell-type identification
- Quarto and R Markdown for report generation
What It Provides
The repository includes:
- Ready-to-use analysis templates
- Downloadable test data for learning and validation
- Dependency installation scripts
- Quick-start documentation for RStudio users
- Standardized workflows across different spatial platforms
Development Status
Projects are labeled with revision tiers:
- Stable: Fully tested and production-ready
- Alpha: Functional but requires additional testing
- Draft: Under active development, may need manual parameter tuning
Why This Matters
Spatial transcriptomics generates complex data requiring specialized analysis approaches. This project:
- Reduces setup time for new spatial transcriptomics projects
- Provides validated workflows following best practices
- Enables reproducible research through standardized templates
- Lowers the barrier to entry for spatial data analysis
- Maintains consistency across different experimental platforms
For more information or to contribute, visit the GitHub repository.
