Numbat is a haplotype-aware CNV caller from single-cell and spatial transcriptomics data. It integrates signals from gene expression, allelic ratio, and population-derived haplotype information to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship.
Numbat can be used to:
- Detect allele-specific copy number variations from scRNA-seq and spatial transcriptomics
- Differentiate tumor versus normal cells in the tumor microenvironment
- Infer the clonal architecture and evolutionary history of profiled tumors.
Numbat does not require paired DNA or genotype data and operates solely on the donor scRNA-seq data (for example, 10x Cell Ranger output). For details of the method, please checkout our paper:
For a complete guide, please see Numbat User Guide.
We appreciate your feedback! Please raise a github issue for bugs, questions and new feature requests. For bug reports, please attach full log, error message, input parameters, and ideally a reproducible example (if possible).