spaSim

DOI: 10.18129/B9.bioc.spaSim  

Spatial point data simulator for tissue images

Bioconductor version: Release (3.17)

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>

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")

 

HTML	R Script	vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiomedicalInformatics, Software, Spatial, StatisticalMethod
Version	1.2.1
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
License	Artistic-2.0
Depends	R (>= 4.2.0)
Imports	ggplot2, methods, stats, dplyr, spatstat.geom, spatstat.random, SpatialExperiment, SummarizedExperiment, RANN
LinkingTo
Suggests	RefManageR, BiocStyle, knitr, testthat (>= 3.0.0), sessioninfo, rmarkdown, markdown
SystemRequirements
Enhances
URL	https://trigosteam.github.io/spaSim/
BugReports	https://support.bioconductor.org/t/spaSim
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	spaSim_1.2.1.tar.gz
Windows Binary	spaSim_1.2.1.zip (64-bit only)
macOS Binary (x86_64)	spaSim_1.2.1.tgz
macOS Binary (arm64)	spaSim_1.2.1.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/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive