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 |
| Reference manual: | numbat.pdf |
| Package source: | numbat_1.4.2.tar.gz |
| Windows binaries: | r-devel: numbat_1.4.2.zip, r-release: numbat_1.4.2.zip, r-oldrel: numbat_1.4.2.zip |
| macOS binaries: | r-devel (arm64): numbat_1.4.2.tgz, r-release (arm64): numbat_1.4.2.tgz, r-oldrel (arm64): numbat_1.4.2.tgz, r-devel (x86_64): numbat_1.4.2.tgz, r-release (x86_64): numbat_1.4.2.tgz, r-oldrel (x86_64): numbat_1.4.2.tgz |
| Old sources: | numbat archive |
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