spaSim
This is the released version of spaSim; for the devel version, see spaSim.
Spatial point data simulator for tissue images
Bioconductor version: Release (3.23)
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("spaSim")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, Software, Spatial, StatisticalMethod |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 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_1.14.0.tar.gz |
| Windows Binary (x86_64) | spaSim_1.14.0.zip |
| macOS Binary (big-sur-x86_64) | spaSim_1.14.0.tgz |
| macOS Binary (sonoma-arm64) | spaSim_1.14.0.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 |