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SRTsim: Simulator for Spatially Resolved Transcriptomics

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.

Version: 0.99.7
Depends: R (≥ 3.5.0), methods
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
Published: 2024-08-21
DOI: 10.32614/CRAN.package.SRTsim
Author: Jiaqiang Zhu ORCID iD [aut, ctb, cre], Lulu Shang ORCID iD [aut], Xiang Zhou ORCID iD [aut]
Maintainer: Jiaqiang Zhu <jiaqiang at umich.edu>
License: GPL (≥ 3)
NeedsCompilation: no
CRAN checks: SRTsim results

Documentation:

Reference manual: SRTsim.pdf
Vignettes: Introduction to SRTsim (source, R code)

Downloads:

Package source: SRTsim_0.99.7.tar.gz
Windows binaries: r-devel: SRTsim_0.99.7.zip, r-release: SRTsim_0.99.7.zip, r-oldrel: SRTsim_0.99.7.zip
macOS binaries: r-release (arm64): SRTsim_0.99.7.tgz, r-oldrel (arm64): SRTsim_0.99.7.tgz, r-release (x86_64): SRTsim_0.99.7.tgz, r-oldrel (x86_64): SRTsim_0.99.7.tgz
Old sources: SRTsim archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=SRTsim to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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