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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:

  1. Detect allele-specific copy number variations from scRNA-seq
  2. Differentiate tumor versus normal cells in the tumor microenvironment
  3. Infer the clonal architecture and evolutionary history of profiled tumors.

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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 paper:

Teng Gao, Ruslan Soldatov, Hirak Sarkar, Adam Kurkiewicz, Evan Biederstedt, Po-Ru Loh, Peter Kharchenko. Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes. Nat Biotechnol (2022).

User Guide

For a complete guide, please see Numbat User Guide.

Questions?

We appreciate your feedback! Please raise a github issue or email us.