Annotation

Tutorials for single-cell cell type annotation.

• Reference-free automated single-cell cell type annotation
  • Data preprocess
  • Automated Annotation
  • Save the annotated dataset
• Reference automated single-cell cell type annotation
  • Data preprocess
  • Automated Annotation
• Consensus annotation with CellVote — PBMC3k
  • Setup: API key for the arbitration step
  • 1) Load the pre-annotated pbmc3k
  • 2) Compare the five annotations on UMAP
  • 3) Compute marker genes per leiden cluster
  • 4) Run CellVote with all five annotation columns
  • 5) Final consensus + per-cluster confidence
  • 6) CellVote confidence (per-cluster consensus score)
  • 7) Per-cluster consensus table (5 methods + final + confidence)
  • 8) Notes
• Mapping Cell Names to the Cell Ontology/Taxonomy
  • Prepared datasets
  • Download the CL Model
  • Prepare the CellOntologyMapper
  • Mapping Celltype
  • Mapping Cell Types with LLM Assistance
  • Cell Taxonomy
  • Mapping Check
• Individual methods
  • Celltype auto annotation with SCSA
  • Automatic cell type annotation with GPT/Other
  • Celltype auto annotation with MetaTiME
  • Using scMulan to annotate cell types in Heart, Lung, Liver, Bone marrow, Blood, Brain, and Thymus
  • 1. load h5ad
  • 2. transform original h5ad with uniformed genes (42117 genes)
  • 3. process uniformed data (simply norm and log1p)
  • 4. load scMulan
  • 5. visualization
  • Celltype annotation migration(mapping) with TOSICA