Haplotype-Aware CNV Analysis from scRNA-Seq R package numbat version 1.5.2 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>. Software 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, 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), Teng Gao <tgaoteng@gmail.com> Comprehensive R Archive Network (CRAN) Teng Gao [cre, aut], Ruslan Soldatov [aut], Hirak Sarkar [aut], Evan Biederstedt [aut], Peter Kharchenko [aut] MIT + file LICENSE (https://CRAN.R-project.org/package=numbat/LICENSE) 2026-02-04 application/tgz https://CRAN.R-project.org/package=numbat doi:10.32614/CRAN.package.numbat