DESCRIPTION

Type: Package
Package: cardelino
Title: Clone Identification from Single Cell Data
Version: 1.1.1
Authors@R: 
    c(person(given = "Jeffrey", 
             family = "Pullin",
             role = "aut",
             email = "jpullin@svi.edu.au"),
      person(given = "Yuanhua",
             family = "Huang",
             role = "aut",
             email = "yuanhua@hku.hk"),
      person(given = "Davis",
             family = "McCarthy",
             role = c("aut", "cre"),
             email = "dmccarthy@svi.edu.au"))
Description: Methods to infer clonal tree configuration for a population of
    cells using single-cell RNA-seq data (scRNA-seq), and possibly other data
    modalities. Methods are also provided to assign cells to inferred clones
    and explore differences in gene expression between clones. These methods
    can flexibly integrate information from imperfect clonal trees inferred
    based on bulk exome-seq data, and sparse variant alleles expressed in
    scRNA-seq data. A flexible beta-binomial error model that accounts for
    stochastic dropout events as well as systematic allelic imbalance is used.
License: GPL-3
URL: https://github.com/single-cell-genetics/cardelino
BugReports: https://github.com/single-cell-genetics/cardelino/issues
Depends: 
    R (>= 4.2),
    stats
Imports: 
    combinat,
    GenomeInfoDb,
    GenomicRanges,
    ggplot2,
    ggtree,
    Matrix,
    matrixStats,
    methods,
    pheatmap,
    snpStats,
    S4Vectors,
    utils,
    VariantAnnotation,
    vcfR
Suggests: 
    BiocStyle,
    foreach,
    knitr,
    pcaMethods,
    rmarkdown,
    testthat,
    VGAM
Enhances:
    doMC
VignetteBuilder: 
    knitr
biocViews: SingleCell, RNASeq, Visualization, Transcriptomics,
    GeneExpression, Sequencing, Software, ExomeSeq
Encoding: UTF-8
NeedsCompilation: yes
RoxygenNote: 7.2.1