EMDomics
Bioc currentEarth Mover's Distance for Differential Analysis of Genomics Data
Release Lineage
Entered 3.1 · Apr 17, 2015
Current · Requires R 4.6
Description
The EMDomics algorithm is used to perform a supervised multi-class analysis to measure the magnitude and statistical significance of observed continuous genomics data between groups. Usually the data will be gene expression values from array-based or sequence-based experiments, but data from other types of experiments can also be analyzed (e.g. copy number variation). Traditional methods like Significance Analysis of Microarrays (SAM) and Linear Models for Microarray Data (LIMMA) use significance tests based on summary statistics (mean and standard deviation) of the distributions. This approach lacks power to identify expression differences between groups that show high levels of intra-group heterogeneity. The Earth Mover's Distance (EMD) algorithm instead computes the "work" needed to transform one distribution into another, thus providing a metric of the overall difference in shape between two distributions. Permutation of sample labels is used to generate q-values for the observed EMD scores. This package also incorporates the Komolgorov-Smirnov (K-S) test and the Cramer von Mises test (CVM), which are both common distribution comparison tests.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
24 18 exported
Complexity
3.9 avg / 17 max
Call network
24 nodes / 7 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
3,189
Files
32
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
18
Internal functions
6
Testing & CI
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.2.1
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
23
First release
2015-04-16
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Sadhika Malladi author maintainer
- Daniel Schmolze author maintainer
- Andrew Beck author
- Sheida Nabavi author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("EMDomics")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.