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dorothea

Bioc current

Collection Of Human And Mouse TF Regulons

v1.23.0 · experiment · GPL-3 + file LICENSE
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Release Lineage

Entered 3.11 · Apr 28, 2020

Current · Requires R 4.6

1.0 In 13 of 49 releases 3.23

Description

DoRothEA is a gene regulatory network containing signed transcription factor (TF) - target gene interactions. DoRothEA regulons, the collection of a TF and its transcriptional targets, were curated and collected from different types of evidence for both human and mouse. A confidence level was assigned to each TF-target interaction based on the number of supporting evidence.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

8 2 exported

Complexity

1.5 avg / 2 max

Call network

8 nodes / 4 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

979

Files

81

Compiled share

0%

Has compiled src

No

Language breakdown

R 328 (33.5%)Tests 185 (18.9%)Docs 270 (27.6%)Vignettes 196 (20%)

API

Exported functions

3

Internal functions

6

Testing & CI

Has tests

Yes

Test-to-code ratio

0.56

testthat edition

–

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Roxygen coverage

66.7%

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

4.0

System requirements

–

C++ standard

–

License

GPL-3 + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

13

First release

2020-08-13

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

–

Dep drift

3

LOC over versions

v3.11: 1,097 LOCv3.12: 1,122 LOCv3.13: 1,265 LOCv3.14: 1,266 LOCv3.15: 907 LOCv3.16: 907 LOCv3.17: 978 LOCv3.18: 979 LOCv3.19: 979 LOCv3.20: 979 LOCv3.21: 979 LOCv3.22: 979 LOCv3.23: 979 LOC

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

Documentation
READMEYes · 461 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 100% structuredCode of conductNoContributing guideNo
Examples that run
100%
Documented parameters
100%
Return-value docs
100%
References docs
0%

Topics

ExperimentData
ExperimentData › OrganismData › Homo_sapiens_Data
ExperimentData › OrganismData › Mus_musculus_Data

Depended on by (5)

Bioconductor (5)

cosmosR easier epiregulon.extra MethReg netZooR

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