spaSim

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see spaSim.

Spatial point data simulator for tissue images

Bioconductor version: 3.18

A suite of functions for simulating spatial patterns of cells in tissue images. Output images are multitype point data in SingleCellExperiment format. Each point represents a cell, with its 2D locations and cell type. Potential cell patterns include background cells, tumour/immune cell clusters, immune rings, and blood/lymphatic vessels.

Author: Yuzhou Feng [aut, cre] , Anna Trigos [aut]

Maintainer: Yuzhou Feng <yuzhou.feng at petermac.org>

Citation (from within R, enter citation("spaSim")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("spaSim")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("spaSim")

vignette HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BiomedicalInformatics, Software, Spatial, StatisticalMethod

Version 1.4.0

In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)

License Artistic-2.0

Depends R (>= 4.2.0)

Imports ggplot2, methods, stats, dplyr, spatstat.geom, spatstat.random, SpatialExperiment, SummarizedExperiment, RANN

System Requirements

URL https://trigosteam.github.io/spaSim/

Bug Reports https://support.bioconductor.org/t/spaSim

Suggests RefManageR, BiocStyle, knitr, testthat (>= 3.0.0), sessioninfo, rmarkdown, markdown

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package spaSim_1.4.0.tar.gz

Windows Binary spaSim_1.4.0.zip (64-bit only)

macOS Binary (x86_64) spaSim_1.4.0.tgz

macOS Binary (arm64) spaSim_1.4.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/spaSim

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/spaSim

Bioc Package Browser https://code.bioconductor.org/browse/spaSim/

Package Short Url https://bioconductor.org/packages/spaSim/

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