Package: scMultiSim
Title: Simulation of Multi-Modality Single Cell Data Guided By Gene
        Regulatory Networks and Cell-Cell Interactions
Version: 1.6.0
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
Config/pak/sysreqs: libglpk-dev libxml2-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:29:36 UTC
RemoteUrl: https://github.com/bioc/scMultiSim
RemoteRef: RELEASE_3_22
RemoteSha: 6add3c1ebeb8a4352a4d691947fa73238d7c72c9
NeedsCompilation: no
Packaged: 2026-01-24 20:33:24 UTC; root
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 4.5.2; ; 2026-01-24 20:35:16 UTC; windows
