spaSim

DOI: 10.18129/B9.bioc.spaSim    

This is the development version of spaSim; to use it, please install the devel version of Bioconductor.

Spatial point data simulator for tissue images

Bioconductor version: Development (3.16)

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 "4.2") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 0.99.3
In Bioconductor since BioC 3.16 (R-4.2)
License Artistic-2.0
Depends R (>= 4.2.0)
Imports ggplot2, methods, stats, dplyr, spatstat.geom, spatstat.random, SpatialExperiment, SummarizedExperiment
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_0.99.3.tar.gz
Windows Binary spaSim_0.99.3.zip
macOS 10.13 (High Sierra) spaSim_0.99.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/spaSim
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/spaSim
Package Short Url https://bioconductor.org/packages/spaSim/
Package Downloads Report Download Stats

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