scSpatialSIM

0.1.4

A Point Pattern Simulator for Spatial Cellular Data

1packages depend

2.9Kdownloads / year

2.3%test coverage

13/13checks pass

Overview

About

Maintained by Fridley LabFirst published 2023-10-124 releasesCRAN page ↗GitHub ↗

Single cell resolution data has been valuable in learning about tissue microenvironments and interactions between cells or spots. This package allows for the simulation of this level of data, be it single cell or ‘spots’, in both a univariate (single metric or cell type) and bivariate (2 or more metrics or cell types) ways. As more technologies come to marker, more methods will be developed to derive spatial metrics from the data which will require a way to benchmark methods against each other. Additionally, as the field currently stands, there is not a gold standard method to be compared against. We set out to develop an R package that will allow users to simulate point patterns that can be biologically informed from different tissue domains, holes, and varying degrees of clustering/colocalization. The data can be exported as spatial files and a summary file (like 'HALO'). https://github.com/FridleyLab/scSpatialSIM/.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("scSpatialSIM", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("FridleyLab/scSpatialSIM")

Development version from FridleyLab/scSpatialSIM. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-scspatialsim

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-scSpatialSIM

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-scSpatialSIM

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 13.3 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.01

2.3%

Coverage · measured lines

92%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 79 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 93%
Return-value docs: 100%
References docs: 0%

Downloads

2.9K

CRAN downloads in the past year

Rank #18,184 · ~8/day · ~243/mo

Releases R versions

Daily download trend is not available in this view yet.

21530 days

61890 days

2.9K1 year

Compare downloads with other packages →

Also on125 r2u20 autocran

Repository

GitHub ↗ fridleylab/scspatialsim

4Stars

2Forks

2Open issues

0Open PRs

6Releases

91Commits

1Contributors

91 commits · Last activity 2026-02-16

Stars over time

2024-05-24 · 42026-07-07 · 4

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/fridleylab/scspatialsim on 2026-07-30.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.00

Imports (12)

dplyr ggplot2 magrittr spatstat.geom crayon ggpubr pbmcapply spatstat.random tidyrutilsmethodsproxy

LinkingTo (0)

none

Suggests (5)

knitr rmarkdown testthat spatialTIME spdep

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

spatialGE

Code & Tests

People & History

People (7)

Maintainer (1)

Fridley Lab

Maintainer

Authors (6)

Jordan Creed

Author

Brooke Fridley

Author, Copyright holder

Author

Author

Author

Author

Author, Copyright holder

Package Timeline

4 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.4Latest
2026-02-16 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.1.3.4
2024-10-01 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.1.3.3
2023-12-19 · diff ↗
0.1.3.2
2023-10-12
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-10-12
Total releases: 4 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.00
Bundled data: 1.1 KB / 1 file
Download size: 1.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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