DESCRIPTION

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