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: 0.99.3
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, spatstat.random, magrittr
Suggests: knitr, rmarkdown, BiocStyle, RefManageR, BiocManager, sessioninfo
Published: 2022-11-20
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
Materials: NEWS
CRAN checks: SRTsim results

Documentation:

Reference manual: SRTsim.pdf
Vignettes: Introduction to SRTsim

Downloads:

Package source: SRTsim_0.99.3.tar.gz
Windows binaries: r-devel: SRTsim_0.99.3.zip, r-release: SRTsim_0.99.3.zip, r-oldrel: SRTsim_0.99.3.zip
macOS binaries: r-release (arm64): SRTsim_0.99.3.tgz, r-oldrel (arm64): SRTsim_0.99.3.tgz, r-release (x86_64): SRTsim_0.99.3.tgz, r-oldrel (x86_64): SRTsim_0.99.3.tgz
Old sources: SRTsim archive

Linking:

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