scRNA-seq workflow

Link to the version1

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Initial Processing

• QC processing and initial filitering
  • UMI cutoff
  • mitochondrial DNA cutoff
  • Doublet Removal (scrublet)
  • Filtered sample plots
  • Subset samples

Integration

• Harmony
  • Preprocessing before integration
  • Harmony integration

Clustering Ananlysis

• UMAP/Clustering/Marker Genes
  • UMAP colored by conditions
  • Number of cells by cluster
  • Sankey plot of 2+ resolutions
  • Marker genes by clusters
• GSEA
  • GSEA by cluster marker genes
    • BP
    • MF
    • CC
  • GSEA info table

Cell type annotation

• Annotation by scType
• Annotation by singleR
• Reference geneset

Trajectory by monocle3

• Trajectory graph

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Further Analysis

• Population changes