spaSim
This is the development version of spaSim; for the stable release version, see spaSim.
Spatial point data simulator for tissue images
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Yuzhou Feng <yuzhou.feng at petermac.org>
citation("spaSim")):
Installation
To install this package, start R (version "4.5") 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")| vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, Software, Spatial, StatisticalMethod |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 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 |
See More
| Suggests | RefManageR, BiocStyle, knitr, testthat (>= 3.0.0), sessioninfo, rmarkdown, markdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | spaSim_1.9.0.tar.gz |
| Windows Binary (x86_64) | spaSim_1.9.0.zip (64-bit only) |
| macOS Binary (x86_64) | spaSim_1.9.0.tgz |
| macOS Binary (arm64) | spaSim_1.9.0.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/ |
| Package Downloads Report | Download Stats |