animalcules
Bioc currentInteractive microbiome analysis toolkit
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
animalcules is an R package for utilizing up-to-date data analytics, visualization methods, and machine learning models to provide users an easy-to-use interactive microbiome analysis framework. It can be used as a standalone software package or users can explore their data with the accompanying interactive R Shiny application. Traditional microbiome analysis such as alpha/beta diversity and differential abundance analysis are enhanced, while new methods like biomarker identification are introduced by animalcules. Powerful interactive and dynamic figures generated by animalcules enable users to understand their data better and discover new insights.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
43 43 exported
Complexity
5 avg / 18 max
Call network
43 nodes / 48 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
6,062
Files
119
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
43
Internal functions
0
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.09
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
2.9%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
15
First release
2019-06-28
Latest release
2026-04-28
Avg cadence
177 days
Cold removal rate
100%
Dep drift
14
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 44 (1 internal)includes a package overview page
- Examples that run
- 98%39 run in a plain check · 1 never run
- Exported functions with examples
- 93%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- animalcules HTML
Repository practices
5 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/wejlab/animalcules on 2026-10-22.
GitHub Pages site last deployed 2019-05-01
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| MAE | – | – | – |
| TB_example_dataset | – | – | – |
| animalcules | list | 4 elements | No other package |
| asthma_example_dataset | – | – | – |
| biom_example | list | 12 elements | No other package |
| toy_data | list | 3 elements | No other package |
Topics
Depended on by (1)
Bioconductor (1)
Suggested by (1)
People
- W. Evan Johnson author maintainer
- Jessica Anderson contractor
- Anthony Federico author
- Yue Zhao author
Cite
Cite this package
Run in R for the authors' entry:
citation("animalcules")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s40168-021-01013-0.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.