Package: scDesign3
Type: Package
Title: A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics
Version: 1.9.0
Authors@R: 
    c(person("Dongyuan", "Song", , "dongyuansong@ucla.edu", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-1114-1215")),
    person("Qingyang", "Wang", , "qw802@g.ucla.edu",  role = c("aut"),
           comment = c(ORCID = "0000-0002-1051-609X")),
    person("Chenxin", "Jiang", , "cflorajiang@g.ucla.edu",  role = c("aut"),
           comment = c(ORCID = "0009-0005-7369-4116")))
Description: We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning interpretable parameters from real data. Using a unified probabilistic model for single-cell and spatial omics data, scDesign3 infers biologically meaningful parameters; assesses the goodness-of-fit of inferred cell clusters, trajectories, and spatial locations; and generates in silico negative and positive controls for benchmarking computational tools.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
Depends: R (>= 4.3.0)
Imports:
    dplyr,
    tibble,
    stats,
    methods,
    mgcv,
    gamlss,
    gamlss.dist,
    SummarizedExperiment,
    SingleCellExperiment,
    mclust,
    mvtnorm,
    parallel,
    pbmcapply,
    umap,
    ggplot2,
    irlba,
    viridis,
    BiocParallel,
    matrixStats,
    Matrix,
    sparseMVN,
    coop
Suggests:
    mvnfast,
    igraph,
    rvinecopulib,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0),
    RefManageR,
    sessioninfo,
    BiocStyle
biocViews:
    Software,
    SingleCell,
    Sequencing,
    GeneExpression,
    Spatial
URL: https://github.com/SONGDONGYUAN1994/scDesign3
BugReports: https://github.com/SONGDONGYUAN1994/scDesign3/issues
RoxygenNote: 7.3.3
Config/testthat/edition: 3
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/scDesign3
git_branch: devel
git_last_commit: f87307f
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
