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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 |
Maintainer: | Jiaqiang Zhu <jiaqiang at umich.edu> |
License: | GPL (≥ 3) |
NeedsCompilation: | no |
CRAN checks: | SRTsim results |
Reference manual: | SRTsim.pdf |
Vignettes: |
Introduction to SRTsim (source, R code) |
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 |
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.