CEMiTool
Bioc currentCo-expression Modules identification Tool
Release Lineage
Entered 3.6 · Oct 31, 2017
Current · Requires R 4.6
Description
The CEMiTool package unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
15 5 exported
Complexity
4.7 avg / 30 max
Call network
15 nodes / 5 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
6,659
Files
102
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
49
Internal functions
10
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.13
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
3.4%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
18
First release
2018-03-23
Latest release
2026-04-28
Avg cadence
175 days
Cold removal rate
100%
Dep drift
17
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 53 (4 internal)
- Examples that run
- 98%46 run in a plain check · 1 never run
- Exported functions with examples
- 98%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 6%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
1 practice detected in the Bioconductor git repository
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| cem | – | – | – |
| expr0 | data.frame | 4,000 × 45 | No other package |
| interactions | data.frame | 185,760 × 2 | No other package |
| sample_annot | data.frame | 45 × 2 | No other package |
Topics
People
- Helder Nakaya author maintainer
- Matheus Bürger author
- Lucas Cardozo author
- Gustavo Ferreira author
- Thiago Hirata author
- Melissa Lever author
- Diogenes Lima author
- Pedro Russo author
Cite
Cite this package
Run in R for the authors' entry:
citation("CEMiTool")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s12859-018-2053-1.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
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.