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Single cell tools for multi-omics data

SVMCellTransfer: Performed reference mapping of cell annotations

scIsoTyper: Single cell 10X VDJ IMGT clonality mapping for downstream single cell multi-omics analysis

scClonetoire: Single cell 10X VDJ IMGT clonality, V/J gene usages, isotype and SHM statistics for plotting for patient groups/downstream analyses

scRepTransition: Single cell quantification of clonal overlap between B, CD4 or CD8 T cell subsets within a sample or between samples

All are written referencing the Sivakumar et al. 2023 study data.