R Observatory: Metrics for dyngen version 1.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

dyngen

1.1.1Package record

A Multi-Modal Simulator for Spearheading Single-Cell Omics Analyses

0packages depend

5.5Kdownloads / year

65.5%test coverage

13/13flavors OK

Overview

About

Maintained by Robrecht CannoodtCRAN page ↗GitHub ↗Website ↗Issues ↗

A novel, multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. 'dyngen' is more flexible than current single-cell simulation engines. It allows better method development and benchmarking, thereby stimulating development and testing of novel computational methods. Cannoodt et al. (2021) doi:10.1038/s41467-021-24152-2.

Changes in 1.1.1

BUG FIX wrap_dataset(): Guard examples (anndata, sce, seurat, dyno) with requireNamespace() checks so CRAN tests do not fail when optional packages are unavailable.

From NEWS.md in the release

Install

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

install.packages("dyngen", 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("dynverse/dyngen")

Development version from dynverse/dyngen. 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-dyngen

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-dyngen

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-dyngen

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 5.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-21
ERROR12 OK, 1 ERROR2026-06-20
OK13 OK2026-06-09

Show 6 earlier changesHide 6 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE10 OK, 4 NOTE2026-03-22
ERROR5 NOTE, 9 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.1

READMEYes · 202 wordsVignettesYes · 2 · staticNEWSYes · 100% structured · mentions 1.1.1Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 33 (1 internal)includes a package overview page
Examples that run: 68%19 run in a plain check · 9 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 93%
Documented parameters: 88%
Return-value docs: 97%
Help pages citing references: 0%

Vignettes (2)

Getting started HTML
Installation instructions HTML

How these are measured

Downloads

5.5K

CRAN downloads in the past year

Rank #4,920 · ~15/day · ~458/mo

Releases R versions

Daily download trend is not available in this view yet.

67430 days

1.7K90 days

5.5K1 year

Compare downloads with other packages →

Also on197 r2u3 autocran

How downloads are counted

Repository

dynverse/dyngen ↗Organization: dynverse

83Stars

6Forks

22Open issues

1Open PRs

3Releases

1,175Commits

5Commit identities

single-cellsingle-cell-analysissingle-cell-omicsbenchmarking

1,175 commits · Last activity 2026-04-01 · +2.5% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 95%
Median days to close, 50 most recently updated closed issues: 82
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-07-14 · 732026-09-24 · 83

How these are measured

PracticesBeta

10 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/dynverse/dyngen on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-04-01 · The repository has a site deploy workflow

pkgdown site last built 2026-04-01

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-03-15
Pull request it wrote: opened by a project member
Commits: at least 1 crediting it in the message

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

27 external dependencies (excludes base and recommended)

Installing dyngen adds 68 packages (39 with compiled code, 56 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, igraph 4.8 MB.

Depends (1)

R >= 4.1.0

Imports (23)

assertthat dplyr dynutils ggplot2 ggraph GillespieSSA2grDevicesgridigraph lmdsMatrixmethodspatchwork pbapply purrr rlangstatstibble tidygraph tidyr tidyselectutilsviridis

LinkingTo (0)

none

Suggests (10)

anndataR ggrepel covr dynwrap R.rsp rmarkdown Seurat SingleCellExperiment SummarizedExperiment testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Robrecht Cannoodt

Wouter Saelens

Author

Releases (9)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.1Latest
record
2026-04-01 · current release · diff ↗
1.1.0
record
2026-03-17 · diff ↗ ·
removed 1 export
%>%
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2022-10-12
1.0.5
record
2022-10-12 · diff ↗
archivedRemoved from CRAN
2022-09-04
issues were not corrected in time
1.0.4
record
2022-08-27 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.3
record
2021-09-20 · diff ↗
1.0.2
record
2021-06-25 · diff ↗ ·
added 1 export
plot_summary
R
R 4.1.0 released · 2021-05-18
1.0.1
record
2021-04-12 · diff ↗ ·
added 2 exports
kinetics_random_distributions, runif_subrange
1.0.0
record
2021-02-23 · diff ↗ ·
added 8 exports
as_anndata, as_dyno, as_list, as_sce, as_seurat, combine_models, get_timings, plot_experiment_dimred

Show 2 earlier eventsHide 2 earlier events

0.4.0
record
2020-09-10
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-09-10
Total releases: 9 / 6 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 427 KB / 3 files
Download size: 2.9 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("dyngen")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1038/s41467-021-24152-2.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for dyngen version 1.1.1 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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