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0.1.0

Getting Started

  • How to install Spatialsnake?
  • Usage of Spatialsnake

Data Ingestion

  • Select your data platform
    • Start with 10x Genomics Visium
    • Visium HD Input Tutorial
    • Visium Segment Input Tutorial
    • Xenium Input Tutorial
    • MERFISH Input Tutorial
    • Stereo-seq Input Tutorial
  • Multi-sample Integration
    • Spatialsnake for multi-sample integration

Main Analysis

  • Core Analysis Workflow
    • Data Integration
    • Preprocessing
    • Clustering
    • Annotation Support
  • Annotation Modules
    • Manual Annotation (manual)
    • Algorithm-Based Annotation (cell2Location)
    • Algorithm-Based Annotation (RCTD)
  • Subcluster Annotation
    • Secondary Clustering (reclustering)
    • Reannotation (reannotation)
  • Downstream Analysis Modules
    • Module 4: Spatial Domain Modeling (cellcharter)
    • Module 5: Spatially Enhanced Clustering (banksy)
    • Module 1: Cell-Cell Communication (cellPhoneDB)
    • Module 3: Cell-Cell Communication (liana)
    • Module 6: Cell Communication Network Analysis (cellchat)
    • Module 2: Regulatory Network Inference (pysenic)
    • Module 7: Differential Expression Comparison (compare_stage)
    • Module 8: Comparative Communication Analysis (compare_stage + cellchat)
  • Utility Tools
    • Splitting Tool (splitting)
    • Merge Tool (merge)
    • Format Conversion Tool (transform)

Reference

  • Contribution/Software Version/Citation
  • Configuration Reference and Practical Tips
    • integrate.yaml Reference
    • preprocess.yaml Reference
    • clustering.yaml Reference
    • annotation_help.yaml Reference
    • reclustering.yaml Reference
    • annotation.yaml Reference
    • advance_analysis.yaml Reference
    • compare_stage.yaml Reference
    • splitting.yaml Reference
    • merge.yaml Reference
    • transform.yaml Reference
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