Description: 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>.
Imports: ape, caTools, data.table, dendextend, dplyr, GenomicRanges,
ggplot2, ggraph, ggtree, glue, igraph, IRanges, logger,
magrittr, methods, optparse, parallel, parallelDist, patchwork,
pryr, purrr, Rcpp, RhpcBLASctl, R.utils, scales, scistreer (>=
1.0.1), stats4, stringr, tibble, tidygraph, tidyr, tidyverse,

Title: Compute the Probability Distribution of the Number of Alleles in
c(person("Maarten", "Kruijver", , "maarten.kruijver@esr.cri.nz", role = c("aut", "cre"),
person("James", "Curran", , "j.curran@auckland.ac.nz", role = c("aut"),
Description: The number of distinct alleles observed in a DNA mixture is informative of the number of contributors to the mixture. The package provides methods for computing the probability distribution of the number of distinct alleles in a mixture for a given set of allele frequencies. The mixture contributors may be related according to a provided pedigree.
Imports: Rcpp (>= 1.0.7), pedtools, ribd, partitions, methods
Suggests: rmarkdown, knitr, testthat (>= 3.0.0), ggplot2
Packaged: 2022-04-27 23:07:07 UTC; mkruijver
Author: Maarten Kruijver [aut, cre] (<https://orcid.org/0000-0002-6890-7632>),