Cogito
Bioc currentCompare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets
Release Lineage
Entered 3.14 · Oct 27, 2021
Current · Requires R 4.6
Description
Biological studies often consist of multiple conditions which are examined with different laboratory set ups like RNA-sequencing or ChIP-sequencing. To get an overview about the whole resulting data set, Cogito provides an automated, complete, reproducible and clear report about all samples and basic comparisons between all different samples. This report can be used as documentation about the data set or as starting point for further custom analysis.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
20 0 exported
Complexity
19.5 avg / 54 max
Call network
20 nodes / 16 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
3,149
Files
17
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
2
Internal functions
20
Testing & CI
Has tests
Yes
Test-to-code ratio
0.04
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
0%
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
4.1
System requirements
–
C++ standard
–
License
LGPL-3
License flags
SPDX valid, OSI approved
History
Versions
10
First release
2021-10-26
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
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
- not tracked
- Return-value docs
- not tracked
- References docs
- 60%
Topics
People
- Annika Bürger maintainer author
Cite
Cite this package
Start here. This is the citation for the package itself.
citation("Cogito")Bioconductor packages have no CRAN DOI. The package landing page is https://bioconductor.org/packages/Cogito.
BibTeX, derived from DESCRIPTION
@Manual{Cogito,
title = {Cogito: Compare genomic intervals tool - Automated, complete,
reproducible and clear report about genomic and epigenomic data
sets},
author = {Bürger, Annika},
year = {2026},
note = {R package version 1.18.0},
url = {https://bioconductor.org/packages/Cogito}
}Derived from the package DESCRIPTION, not from a citation file the authors wrote. If they publish one later, prefer it.
This is the citation for the package. It is not a citation for the R Observatory.
Cite this page
Use this when the claim is about a measurement on this page.
BibTeX
@misc{robservatoryCogito,
author = {Balamuta, James Joseph},
title = {{R} {Observatory}: Metrics for {Cogito} version 1.18.0},
year = {2026},
publisher = {HJJB, LLC},
url = {https://r-observatory.thecoatlessprofessor.com/bioc/Cogito},
note = {Data set. Data release v2026-08-05}
}APA
Balamuta, J. J. (2026). R Observatory: Metrics for Cogito version 1.18.0 [Data set]. HJJB, LLC. Data release v2026-08-05. https://r-observatory.thecoatlessprofessor.com/bioc/CogitoRIS
TY - DATA
AU - Balamuta, James Joseph
TI - R Observatory: Metrics for Cogito version 1.18.0
PY - 2026
PB - HJJB, LLC
N1 - Data release v2026-08-05
UR - https://r-observatory.thecoatlessprofessor.com/bioc/Cogito
ER - In prose
These package metrics were obtained from the R Observatory (Balamuta, 2026), data release v2026-08-05, https://r-observatory.thecoatlessprofessor.com/bioc/Cogito.Bound to data release v2026-08-05, which is what makes the numbers on this page reproducible. See how to cite.