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: 1.4.2 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: 2024-09-20 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 + file LICENSE 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 Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=numbat to link to this page.
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