SDAS Manual
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  • Stereo Data Analysis Solution (SDAS) User Manual
    • Software Introduction
    • Installation Guide
    • Quick Start
    • Instructions for Each Functional Module
      • SDAS Input Data Format Description
      • Performance Test Environment and Data Description
      • Data Processing
        • Introduction
        • Input File Example
        • Command Description
      • Cell Type Annotation
        • Introduction
        • h5ad Data Format Description
        • cell2location Algorithm
          • Build Single-cell Reference Data
          • Cell Annotation
        • RCTD Algorithm
        • Tangram Algorithm
        • SCimilarity Algorithm
          • Build Single-cell Reference Data (Optional)
          • Cell Annotation
        • SPOTlight Algorithm
        • Performance Test
      • Spatial Domain Identification
        • Introduction
        • h5ad Data Format Description
        • graphST Algorithm
        • Performance Test
      • Cellular Neighborhood Analysis
        • Introduction
        • Single Cell Type Mode
        • Cell Type Score Mode
        • Performance Test
      • CNV Analysis
        • Introduction
        • Input File Example
        • InferCNV Algorithm
        • Performance Test
      • Spatial Gene Co-expression
        • Introduction
        • Input File Example
        • hdWGCNA Algorithm
        • Hotspot Algorithm
        • NeST Algorithm
        • Performance Test
      • Differential Gene Analysis
        • Introduction
        • Input File Example
        • Single-cell/pseudobulk Differential Analysis
        • Performance Test
      • Gene Set Enrichment Analysis
        • Introduction
        • Input File Example
        • GSEA Algorithm
        • GSVA Algorithm
        • Enrichr Algorithm
        • Prerank Algorithm
        • Performance Test
      • Protein Interaction Network Analysis
        • Introduction
        • Input File Example
        • GN/MCL/Kmeans Clustering
      • Cell Communication Analysis
        • Introduction
        • Input File Example
        • cellchat Algorithm
        • cellphonedb Algorithm
        • Performance Test
      • Trajectory Analysis
        • Introduction
        • Input File Example
        • monocle3 Algorithm
        • Performance Test
      • Transcription Factor Analysis
        • Introduction
        • Input File Example
        • pyscenic Algorithm
        • Performance Test
      • Cell-type Spatial Relationship Analysis
        • Introduction
        • Input File Example
        • Squidpy Algorithm
        • CRAWDAD Algorithm
        • Performance Test
      • Public Bulk Database Validation
        • Introduction
        • Immune Infiltration Analysis Module
        • Gene Set Scoring Module
        • Survival Analysis Module
    • Pipeline Example
      • Cluster Submission Mode​
      • ​​Standalone Mode​
    • Release Notes
    • Support
      • Frequently Asked Questions
      • SDAS Log and Exit Code Specification
      • SAW aggr (alpha ver.) Pipeline Introduction
      • Reference and Github
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  1. Stereo Data Analysis Solution (SDAS) User Manual
  2. Instructions for Each Functional Module

Spatial Gene Co-expression

IntroductionInput File ExamplehdWGCNA AlgorithmHotspot AlgorithmNeST AlgorithmPerformance Test
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Last updated 13 days ago