CytoSimplex

0.2.0

Simplex Visualization of Cell Fate Similarity in Single-Cell Data

0packages depend

6.7Kdownloads / year

59.2%test coverage

13/13checks pass

Overview

About

Maintained by Yichen WangFirst published 2023-12-133 releasesCRAN page ↗GitHub ↗

Create simplex plots to visualize the similarity between single-cells and selected clusters in a 1-/2-/3-simplex space. Velocity information can be added as an additional layer. See Liu J, Wang Y et al (2023) doi:10.1093/bioinformatics/btaf119 for more details.

Install

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

install.packages("CytoSimplex", 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("welch-lab/CytoSimplex")

Development version from welch-lab/CytoSimplex. 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-cytosimplex

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-CytoSimplex

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-CytoSimplex

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

Health

CRAN checks

13OK

Slowest check: 7.5 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.11

59.2%

Coverage · measured lines

100%

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 178 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 47%
Documented parameters: 96%
Return-value docs: 100%
References docs: 15%

Downloads

6.7K

CRAN downloads in the past year

Rank #6,280 · ~18/day · ~562/mo

Releases R versions

Daily download trend is not available in this view yet.

37730 days

1.6K90 days

6.7K1 year

Compare downloads with other packages →

Also on432 r2u29 autocran

Repository

GitHub ↗ welch-lab/cytosimplex

6Stars

2Forks

1Open issues

0Open PRs

3Releases

76Commits

3Contributors

76 commits · Last activity 2025-04-23 · 0% stars, 30d

Stars over time

2025-04-17 · 52026-07-07 · 6

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/welch-lab/cytosimplex on 2026-07-19.

Continuous integration (1)

GitHub Actions

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

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Depends (4)

R >= 3.6statsmethodsgrDevices

Imports (9)

cli ggplot2Matrixplot3D plotly RColorBrewer Rcpp rlang viridis

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (10)

hdf5r knitr magick patchwork rmarkdown Seurat SeuratObject SingleCellExperiment SummarizedExperiment testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Yichen Wang

Author, Maintainer

Authors (2)

Yichen Wang

Author, Maintainer

Jialin Liu

Author

Joshua Welch

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.2.0Latest
2025-04-23 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.1.1
2023-12-15 · diff ↗
0.1.0
2023-12-13
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-12-13
Total releases: 3 / 3 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.6
Bundled data: 685 KB / 3 files
Download size: 1.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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