scHLAcount

Allele-specific HLA expression from single-cell gene expression data | Count HLA alleles in single-cell RNA-seq data | scHLAcount allows you to count molecules in single-cell RNA-seq data for class I genes HLA-A, B, and C; and class II genes DPA1, DPB1, DRA1, DRB1, DQA1, and DQB1 using a personalized reference genome. You can either use provided HLA types determined by alternative methods or call HLA types with this tool then quantify against those calls. See the Using scHLAcount section for more details