COTAN
Bioc currentCOexpression Tables ANalysis
Release Lineage
Entered 3.15 · Apr 27, 2022
Current · Requires R 4.6
Description
Statistical and computational method to analyze the co-expression of gene pairs at single cell level. It provides the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts' distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can effectively assess the correlated or anti-correlated expression of gene pairs. It provides a numerical index related to the correlation and an approximate p-value for the associated independence test. COTAN can also evaluate whether single genes are differentially expressed, scoring them with a newly defined global differentiation index. Moreover, this approach provides ways to plot and cluster genes according to their co-expression pattern with other genes, effectively helping the study of gene interactions and becoming a new tool to identify cell-identity marker genes.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
119 88 exported
Complexity
5.4 avg / 49 max
Call network
119 nodes / 253 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
24,655
Files
105
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
88
Internal functions
24
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.17
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
9
First release
2022-04-26
Latest release
2026-05-20
Avg cadence
185 days
Cold removal rate
100%
Dep drift
37
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 23
- Examples that run
- 100%17 run in a plain check (1 of them under a condition)
- Exported functions with examples
- 83%
- Documented parameters
- 97%
- Return-value docs
- 100%
- Help pages citing references
- 4%
Updated package to support R version 4.6 and Roxygen 8.0
From NEWS.md in the release
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/seriph78/cotan on 2026-10-11.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| ERCCraw | data.frame | 92 × 1,016 | No other package |
| raw.dataset | data.frame | 2,001 × 815 | No other package |
| test.dataset | data.frame | 600 × 1,000 | No other package |
| test.dataset.clusters1 | factor | 1,000 elements | No other package |
| test.dataset.clusters2 | factor | 1,000 elements | No other package |
| vignette.cells.origin | factor | 2,000 elements | No other package |
| vignette.merge.clusters | factor | 1,783 elements | No other package |
| vignette.split.clusters | factor | 1,783 elements | No other package |
Topics
People
- Galfrè Silvia Giulia author maintainer
- Priami Corrado author
- Puttini Daniel author
- Cremisi Federico author
- Morandin Francesco author
- Helmer-Citterich Manuela author
- Fantozzi Marco author
- Pietrosanto Marco author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("COTAN")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.