Initial Processing

• Raw data processing
  
  • cellranger
    
  • doublet removal
    
    
• Raw data filitering by UMI & mitochondrial content
  
  
  
  

UMAP/Clustering

• UMAP/Clustering
  
  
  
  
• Simple Gene Ontology analysis by cluster marker genes
  
  
  
  

Marker gene Analyais

• Marker genes summary report
  
  
  
  
  
  
  

Differentially Expressed Genes Analyais

• DEG report
  
  
  
  

Cell Type annotation

• Immune Cell Type Annotation by scType
  
  
  

• Manual Annotation by marker genes
  
  
  
  

Functional analysis

• Population shift
  
  

• Gene signature scoring
  

  • UCell
    

• scGSVA
  • scGSVA (single-cell Gene Set Variation Analysis)
  • An unsupervised, gene set enrichment method that estimates the activation states of gene sets at the single-cell level