Numbat is a haplotype-aware CNV caller from single-cell 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
- 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-data data (for example, 10x Cell Ranger output). For details of the method, please checkout our preprint:
Teng Gao, Ruslan Soldatov, Hirak Sarkar, Adam Kurkiewicz, Evan Biederstedt, Po-Ru Loh, Peter Kharchenko. Haplotype-enhanced inference of somatic copy number profiles from single-cell transcriptomes. bioRxiv 2022.
For a complete guide, please see Numbat User Guide.
We appreciate your feedback! Please raise a github issue or email us.