DESCRIPTION

Package: scMultiSim
Title: Simulation of Multi-Modality Single Cell Data Guided By Gene Regulatory Networks and Cell-Cell Interactions
Version: 1.1.10
Authors@R:
    c(person(given = "Hechen",
             family = "Li",
             role = c("aut", "cre"),
             email = "hli691@gatech.edu",
             comment = c(ORCID = "0000-0003-4907-429X")),
      person(given = "Xiuwei",
             family = "Zhang",
             email = "zhangxiuwei03@gmail.com",
             role = "aut"),
      person(given = "Ziqi",
             family = "Zhang",
             email = "ziqi.zhang@gatech.edu",
             role = "aut"),
      person(given = "Michael",
             family = "Squires",
             email = "squiresmf@gatech.edu",
             role = "aut"))
Description:
    scMultiSim simulates paired single cell RNA-seq, single cell ATAC-seq and RNA velocity data,
    while incorporating mechanisms of gene regulatory networks, chromatin accessibility and
    cell-cell interactions. It allows users to tune various parameters controlling the
    amount of each biological factor, variation of gene-expression levels,
    the influence of chromatin accessibility on RNA sequence data, and so on.
    It can be used to benchmark various computational methods for single cell multi-omics data,
    and to assist in experimental design of wet-lab experiments.
License: Artistic-2.0
Encoding: UTF-8
RoxygenNote: 7.3.1
Depends:
    R (>= 4.4.0)
Imports:
    foreach,
    rlang,
    dplyr,
    ggplot2,
    Rtsne,
    ape,
    MASS,
    matrixStats,
    phytools,
    KernelKnn,
    gplots,
    zeallot,
    crayon,
    assertthat,
    igraph,
    methods,
    grDevices,
    graphics,
    stats,
    utils,
    markdown,
    SummarizedExperiment,
    BiocParallel
Suggests:
    knitr,
    rmarkdown,
    roxygen2,
    shiny,
    testthat (>= 3.0.0)
biocViews: SingleCell, Transcriptomics, GeneExpression, Sequencing, ExperimentalDesign
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
BugReports: https://github.com/ZhangLabGT/scMultiSim/issues
URL: https://zhanglabgt.github.io/scMultiSim/
Config/testthat/edition: 3