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 |