cogeqc
Bioc currentSystematic quality checks on comparative genomics analyses
Release Lineage
Entered 3.15 · Apr 27, 2022
Current · Requires R 4.6
Description
cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualization functions to explore QC summary statistics.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
30 24 exported
Complexity
2.6 avg / 9 max
Call network
30 nodes / 15 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
4,253
Files
88
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
24
Internal functions
6
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.18
testthat edition
3
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
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
4.2.0
System requirements
1
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
9
First release
2022-10-11
Latest release
2026-04-28
Avg cadence
161 days
Cold removal rate
–
Dep drift
5
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 97%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 19%
Topics
People
- FabrÃcio Almeida-Silva author maintainer
- Yves Van de Peer author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("cogeqc")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.