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 
[aut, ctb, cre],
Lulu Shang [aut],
Xiang Zhou [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-devel (arm64): SRTsim_0.99.7.tgz, r-release (arm64): SRTsim_0.99.7.tgz, r-oldrel (arm64): SRTsim_0.99.7.tgz, r-devel (x86_64): 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:
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