Package: scMultiSim
Title: Simulation of Multi-Modality Single Cell Data Guided By Gene
        Regulatory Networks and Cell-Cell Interactions
Version: 1.4.0
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
git_url: https://git.bioconductor.org/packages/scMultiSim
git_branch: RELEASE_3_21
git_last_commit: 0b33ee8
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-16 03:44:40 UTC; biocbuild
Author: Hechen Li [aut, cre] (ORCID: <https://orcid.org/0000-0003-4907-429X>),
  Xiuwei Zhang [aut],
  Ziqi Zhang [aut],
  Michael Squires [aut]
Maintainer: Hechen Li <hli691@gatech.edu>
Built: R 4.5.0; ; 2025-04-16 15:28:19 UTC; windows
