Package: numbat

Title: Haplotype-Aware CNV Analysis from scRNA-Seq

URL: https://github.com/kharchenkolab/numbat/, https://kharchenkolab.github.io/numbat/

Version: 1.4.2

Authors@R: c(person("Teng","Gao", email="tgaoteng@gmail.com", role=c("cre", "aut")), person("Ruslan", "Soldatov", email="soldatr@mskcc.org", role="aut"), person("Hirak", "Sarkar", email="hirak_sarkar@hms.harvard.edu", role="aut"), person("Evan", "Biederstedt", email="evan.biederstedt@gmail.com", role="aut"), person("Peter", "Kharchenko", email = "peter_kharchenko@hms.harvard.edu", role = "aut"))

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>.

License: MIT + file LICENSE

Encoding: UTF-8

LazyData: true

Depends:

R (>= 4.1.0), Matrix

biocViews:

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

Suggests:

ggrastr,

ggrepel,

knitr,

matrixStats,

testthat (>= 3.0.0),

Config/testthat/edition: 3

LinkingTo: Rcpp, RcppArmadillo, roptim

NeedsCompilation: yes

SystemRequirements: GNU make

Author: Teng Gao [cre, aut], Ruslan Soldatov [aut], Hirak Sarkar [aut], Evan Biederstedt [aut], Peter Kharchenko [aut]

Maintainer: Teng Gao <tgaoteng@gmail.com>

RoxygenNote: 7.3.2