scImmuCC - Single-cell Immune Cell Classification

Hierarchical layered classification method specifically designed for single-cell RNA-seq data. Provides Layer 1/2/3 cell type identification with visualization outputs.

Supported File Formats
  • CSV/TXT: Gene expression matrix (genes × cells)
  • RDS: R Seurat object
  • H5AD: AnnData object (scanpy)
  • H5Seurat: Seurat object in HDF5 format
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Supported: CSV, TXT, RDS, H5AD, H5Seurat

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What is scImmuCC?

scImmuCC is a hierarchical layered classification method specifically designed for single-cell RNA-seq data. It provides:

  • Layer 1: Major immune cell lineage classification
  • Layer 2: Refined cell subtype identification
  • Layer 3: Detailed cell state characterization

Results include classification tables (CSV) and visualizations (tSNE, UMAP, heatmaps).

Citation

If you use scImmuCC in your research, please cite:

Ying Jiang, Ziyi Chen, Na Han, Jingzhe Shang, Aiping Wu. sc-ImmuCC: hierarchical annotation for immune cell types in single-cell RNA-seq. Bioinformatics, 2022, 38(18): 4369-4376. DOI: 10.1093/bioinformatics/btac534