A computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. 'numbat' integrates signals from gene expression, allelic ratio, and population haplotype structures 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 single-cells; 2. differentiate tumor versus normal cells in the tumor microenvironment; 3. infer the clonal architecture and evolutionary history of profiled tumors. 'numbat' does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). Additional examples and documentations are available at <https://kharchenkolab.github.io/numbat/>. For details on the method please see Gao et al. Nature Biotechnology (2022) <doi:10.1038/s41587-022-01468-y>.
| Version: | 1.5.1 |
| Depends: | R (≥ 4.1.0),Matrix |
| Imports: | ape,caTools,data.table,dendextend,dplyr (≥ 1.1.1),GenomicRanges,ggplot2,ggraph,ggtree,glue,hahmmr,igraph,IRanges,logger,magrittr, methods,optparse, parallel,parallelDist,patchwork,pryr,purrr,Rcpp,RhpcBLASctl,R.utils,scales,scistreer (≥ 1.1.0), stats4,stringr,tibble,tidygraph,tidyr (≥ 1.3.0),vcfR,zoo |
| LinkingTo: | Rcpp,RcppArmadillo,roptim |
| Suggests: | ggrastr,ggrepel,knitr,matrixStats,testthat (≥ 3.0.0) |
| Published: | 2025-10-21 |
| DOI: | 10.32614/CRAN.package.numbat |
| Author: | Teng Gao [cre, aut], Ruslan Soldatov [aut], Hirak Sarkar [aut], Evan Biederstedt [aut], Peter Kharchenko [aut] |
| Maintainer: | Teng Gao <tgaoteng at gmail.com> |
| License: | MIT + fileLICENSE |
| URL: | https://github.com/kharchenkolab/numbat/,https://kharchenkolab.github.io/numbat/ |
| NeedsCompilation: | yes |
| SystemRequirements: | GNU make |
| Citation: | numbat citation info |
| Materials: | README,NEWS |
| CRAN checks: | numbat results |