dorothea
Bioc currentCollection Of Human And Mouse TF Regulons
Release Lineage
Entered 3.11 · Apr 28, 2020
Current · Requires R 4.6
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.
None published for Bioconductor
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
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
979
Files
75
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
3
Internal functions
6
Testing
Has tests
Yes
Test-to-code ratio
0.56
testthat edition
–
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
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 9 (2 internal)includes a package overview page
- Examples that run
- 100%3 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- DoRothEA regulons. HTML
Repository practices
6 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/saezlab/dorothea on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows
GitHub Pages site last deployed 2024-02-24 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| dorothea_hs | tibble | 454,504 × 4 | No other package |
| dorothea_hs_pancancer | tibble | 213,230 × 4 | No other package |
| dorothea_mm | tibble | 386,758 × 4 | No other package |
| dorothea_mm_pancancer | tibble | 187,931 × 4 | No other package |
| entire_database | – | – | – |
| gene_annotation | tibble | 151,785 × 4 | No other package |
| hgnc_mgi_annotation | tibble | 24,333 × 2 | No other package |
| hsa_uniprot_20180314 | data.frame | 20,316 × 4 | No other package |
| tf_annotation | tibble | 1,639 × 2 | No other package |
| uniprot_annotation | tibble | 20,162 × 4 | No other package |
Topics
Depended on by (2)
Suggested by (3)
People
- Pau Badia-i-Mompel maintainer
- Minoo Ashtiani contributor
- Daniel Dimitrov author
- Attila Gabor contributor
- Luz Garcia-Alonso author
- Christian H. Holland author
- Alberto Valdeolivas contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("dorothea")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1101/gr.240663.118, 10.1093/bioadv/vbac016, 10.1101/2023.03.30.534849.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.