R Observatory: Metrics for destiny version 3.26.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

destiny

Bioc current

Creates diffusion maps

v3.26.0 · Package record · software · GPL-3

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.2 · Oct 14, 2015

Current · Requires R 4.6

1.0 In 22 of 49 releases 3.23

Description

Create and plot diffusion maps.

Advisories

None published for Bioconductor

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

100 22 exported

Complexity

4.8 avg / 57 max

Call network

100 nodes / 96 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

How coverage is measured·How the call graph is built

Code

Structure

Lines of code

7,411

Files

110

Compiled share

4.4%

Has compiled src

Yes

Language breakdown

R 3,966 (53.5%)C/C++/src 328 (4.4%)Tests 322 (4.3%)Docs 1,916 (25.9%)Vignettes 879 (11.9%)

API

Exported functions

40

Internal functions

68

Recent export changes

v3.7+1 plot_differential_map

v3.6+1 find_knn

Testing

Has tests

Yes

Test-to-code ratio

0.08

testthat edition

–

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

7.1%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.4.0

System requirements

1 externalC++11

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

22

First release

2015-10-13

Latest release

2026-04-28

Avg cadence

183 days

Cold removal rate

100%

Dep drift

24

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

In the Bioconductor 3.23 release

README· In the Bioconductor git repository, left out of the releaseVignettesYes · 6 · dynamicNEWSYes · 100% structuredCitation fileYes · cites a publication

Help pages: 31includes a package overview page
Examples that run: 100%28 run in a plain check
Exported functions with examples: 95%
Documented parameters: 91%
Return-value docs: 100%
Help pages citing references: 3%

Also includes 1 demo script (run with demo())

Vignettes (6)

How these are measured

Repository practices

Upstream repositoryBeta

9 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/theislab/destiny on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (2)

GitHub Pages site last deployed 2023-12-28 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting

Lint, format, editor (3)

lintrVS CodeRStudio project

Show all practicesHide 1 practice

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v4 (2026-10-20)

Datasets

Bundled datasets · 2

Name	Class	Size	Also in
guo	–	–	–
guo_norm	–	–	–

All of destiny's data objects

Topics

Software › ResearchField › CellBiology

Software › AssayDomain › CellBasedAssays

Software › StatisticalMethod › Clustering

Software

Software › WorkflowStep › Visualization

Maintainer: Philipp Angerer

Available on

CRANr2uBioconductorautoCRANCOPR

Depended on by (5)

Bioconductor (5)

cytofkit CytoTree dandelionR flowSpy phemd

Suggested by (3)

CelliD CellTrails monocle

People

Philipp Angerer maintainer author
Florian Büttner contributor
Maren Büttner contributor
Laleh Haghverdi contributor
Carsten Marr contributor
Fabian Theis contributor

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("destiny")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 destiny version 3.26.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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