numbat: Haplotype-Aware CNV Analysis from scRNA-Seq

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 <>. For details on the method please see Gao et al. Nature Biotechnology (2022) <doi:10.1038/s41587-022-01468-y>.

Version: 1.4.0
Depends: R (≥ 4.1.0), Matrix
Imports: ape, caTools, data.table, dendextend, dplyr, 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, vcfR, zoo
LinkingTo: Rcpp, RcppArmadillo, roptim
Suggests: ggrastr, ggrepel, knitr, matrixStats, testthat (≥ 3.0.0)
Published: 2024-02-23
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>
License: MIT + file LICENSE
NeedsCompilation: yes
SystemRequirements: GNU make
Citation: numbat citation info
Materials: README NEWS
CRAN checks: numbat results


Reference manual: numbat.pdf


Package source: numbat_1.4.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): numbat_1.4.0.tgz, r-oldrel (arm64): numbat_1.4.0.tgz, r-release (x86_64): numbat_1.4.0.tgz, r-oldrel (x86_64): numbat_1.4.0.tgz
Old sources: numbat archive


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