DESCRIPTION

Package: SRTsim
Type: Package
Title: Simulator for Spatially Resolved Transcriptomics
Version: 0.99.8
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
Roxygen: list(markdown = TRUE)
Imports: concaveman,sf,sp,spatstat.geom,parallel,pdist,MASS,S4Vectors,stats,Matrix,Morpho,matrixStats,plotly,shiny,viridis,shinyBS, ggplot2, ggpubr, DT, spatstat.random,magrittr,FNN,dplyr, magick,shinydashboard
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'