Type: Package
Package: cardelino
Title: Clone Identification from Single Cell Data
Version: 1.13.0
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
Config/pak/sysreqs: libcairo2-dev libfontconfig1-dev libfreetype6-dev
        make libbz2-dev libicu-dev liblzma-dev libpng-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:19:32 UTC
RemoteUrl: https://github.com/bioc/cardelino
RemoteRef: HEAD
RemoteSha: d0e349d1138fb04d3381eb3804646c01185ead15
Packaged: 2026-03-10 08:08:25 UTC; root
Author: Jeffrey Pullin [aut],
  Yuanhua Huang [aut],
  Davis McCarthy [aut, cre]
Maintainer: Davis McCarthy <dmccarthy@svi.edu.au>
Built: R 4.6.0; ; 2026-03-10 08:10:50 UTC; windows
