variancePartition
Bioc currentQuantify and interpret drivers of variation in multilevel gene expression experiments
Release Lineage
Entered 3.2 · Oct 14, 2015
Current · Requires R 4.6
Description
Quantify and interpret multiple sources of biological and technical variation in gene expression experiments. Uses a linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables. Includes dream differential expression analysis for repeated measures.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
71 23 exported
Complexity
7.2 avg / 120 max
Call network
71 nodes / 51 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
15,121
Files
160
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
38
Internal functions
48
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
25%
Unsafe pattern score
0
Dep constraint coverage
17.2%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3.0
System requirements
–
C++ standard
–
License
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
22
First release
2016-03-03
Latest release
2026-04-28
Avg cadence
194 days
Cold removal rate
100%
Dep drift
30
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 69 (4 internal)
- Examples that run
- 100%34 run in a plain check
- Exported functions with examples
- 82%
- Documented parameters
- 97%
- Return-value docs
- 84%
- Help pages citing references
- 6% with a bibliography file
Repository practices
2 development-tooling and community-health practices detected across 1 family in the upstream repository
Checks run against github.com/diseaseneurogenomics/variancepartition on 2026-10-18.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| countMatrix | matrix | 19,364 × 24 | No other package |
| geneCounts | matrix | 200 × 100 | No other package |
| geneExpr | matrix | 200 × 100 | No other package |
| info | data.frame | 100 × 6 | No other package |
| metadata | data.frame | 24 × 5 | No other package |
Topics
Depended on by (5)
Suggested by (1)
People
- Gabriel Hoffman author maintainer
Cite
Cite this package
Run in R for the authors' entry:
citation("variancePartition")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1101/2023.03.17.533005, 10.1093/bioinformatics/btaa687, 10.1186/s12859-016-1323-z.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.