Package: SRTsim
Type: Package
Title: Simulator for Spatially Resolved Transcriptomics
Version: 0.99.7
Date: 2024-08-14
Authors@R: c(
  person(given = "Jiaqiang", family = "Zhu", email = "jiaqiang@umich.edu", role = c("aut","ctb","cre"), comment = c(ORCID = "0000-0002-1455-0041")),
  person(given = "Lulu", family = "Shang", email = "shanglu@umich.edu", role = "aut", comment = c(ORCID = "0000-0002-2480-3065")),
  person(given = "Xiang", family = "Zhou", email = "xzhousph@umich.edu", role = "aut", comment = c(ORCID = "0000-0002-4331-7599"))
  )
Maintainer: Jiaqiang Zhu <jiaqiang@umich.edu>
Description: An independent, reproducible, and flexible Spatially Resolved Transcriptomics (SRT) simulation framework that can be used to facilitate the development of SRT analytical methods for a wide variety of SRT-specific analyses. It utilizes spatial localization information to simulate SRT expression count data in a reproducible and scalable fashion. Two major simulation schemes are implemented in 'SRTsim': reference-based and reference-free.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
Imports:
        concaveman,sf,sp,spatstat.geom,parallel,pdist,MASS,S4Vectors,stats,Matrix,Morpho,matrixStats,plotly,shiny,viridis,shinydashboard,dashboardthemes,shinyBS,
        ggplot2, ggpubr, DT, spatstat.random,magrittr,FNN,dplyr, magick
Suggests: knitr,rmarkdown,BiocStyle,RefManageR,BiocManager,sessioninfo
VignetteBuilder: knitr
Depends: R (>= 3.5.0), methods
NeedsCompilation: no
Collate: 'SRTaffine.R' 'SRTcount.R' 'SRTfit.R' 'SRTmodels.R'
        'SRTsim_class.R' 'body.R' 'compareSRT.R' 'createSRT.R' 'data.R'
        'globals.R' 'reGenCountshiny.R' 'runapp.R' 'server.R'
        'shiny2srt.R' 'sidebar.R' 'simSRTLocs.R' 'subsetSRT.R'
        'SRTcci.R' 'ui.R' 'utilies_func.R' 'visualize_gene.R'
        'visualize_metrics.R'
Packaged: 2024-08-20 21:02:00 UTC; jiaqiangzhu
Author: Jiaqiang Zhu [aut, ctb, cre] (<https://orcid.org/0000-0002-1455-0041>),
  Lulu Shang [aut] (<https://orcid.org/0000-0002-2480-3065>),
  Xiang Zhou [aut] (<https://orcid.org/0000-0002-4331-7599>)
Repository: CRAN
Date/Publication: 2024-08-21 08:10:05 UTC
Built: R 4.4.3; ; 2025-11-12 05:56:11 UTC; windows
