Package: spaSim 1.15.0

Yuzhou Feng

spaSim: Spatial point data simulator for tissue images

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.

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

spaSim_1.15.0.tar.gz
spaSim_1.15.0.zip(r-4.7)spaSim_1.15.0.zip(r-4.6)spaSim_1.15.0.zip(r-4.5)
spaSim_1.15.0.tgz(r-4.6-any)spaSim_1.15.0.tgz(r-4.5-any)
spaSim_1.15.0.tar.gz(r-4.7-any)spaSim_1.15.0.tar.gz(r-4.6-any)
spaSim_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
spaSim/json (API)
NEWS

# Install 'spaSim' in R:
install.packages('spaSim', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/trigosteam/spasim/issues

Pkgdown/docs site:https://trigosteam.github.io

Datasets:
  • bg1 - Background cells

On BioConductor:spaSim-1.15.0(bioc 3.24)spaSim-1.14.0(bioc 3.23)

statisticalmethodspatialbiomedicalinformatics

5.27 score 2 stars 31 scripts 319 downloads 10 exports 77 dependencies

Last updated from:2cc39a7394. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE192
linux-devel-x86_64NOTE435
source / vignettesOK242
linux-release-x86_64NOTE376
macos-release-arm64NOTE210
macos-oldrel-arm64NOTE202
windows-develNOTE323
windows-releaseNOTE332
windows-oldrelNOTE285
wasm-releaseOK141

Exports:multiple_background_imagesmultiple_images_with_clustersmultiple_images_with_immune_ringssimulate_background_cellssimulate_clusterssimulate_double_ringssimulate_immune_ringssimulate_mixingsimulate_stripesTIS

Dependencies:abindaskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11curlDBIdbplyrDelayedArraydeldirdplyrfarverfastmapfilelockgenericsGenomicRangesggplot2gluegtablehttr2IRangesisobandlabelinglatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigpolyclippurrrR6RANNrappdirsRColorBrewerRcpprjsonrlangRSQLiteS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraySpatialExperimentspatstat.dataspatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsystensortibbletidyrtidyselectutf8vctrsviridisLitewithrXVector

spaSim vignette

Yuzhou Feng, Anna Trigos

Rendered fromvignette.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2022-11-29
Started: 2022-02-17