tigre
Bioc currentTranscription factor Inference through Gaussian process Reconstruction of Expression
Release Lineage
Entered 2.6 · Apr 23, 2010
Current · Requires R 4.6
Description
The tigre package implements our methodology of Gaussian process differential equation models for analysis of gene expression time series from single input motif networks. The package can be used for inferring unobserved transcription factor (TF) protein concentrations from expression measurements of known target genes, or for ranking candidate targets of a TF.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
207 0 exported
Complexity
5.1 avg / 41 max
Call network
207 nodes / 212 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
9,362
Files
59
Compiled share
3.1%
Has compiled src
Yes
Language breakdown
API
Exported functions
157
Internal functions
48
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
6
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.11.0
System requirements
–
C++ standard
–
License
AGPL-3
License flags
SPDX valid, OSI approved
History
Versions
33
First release
2010-09-20
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
–
Dep drift
6
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 27includes a package overview page
- Examples that run
- 68%17 run in a plain check · 6 never run · 2 hold no code
- Exported functions with examples
- 100%
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 19%
- tigre User Guide PDF
Repository practices
Checks run against github.com/ahonkela/tigre on 2026-10-11.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| drosophila_gpsim_fragment | – | – | – |
| drosophila_mmgmos_fragment | – | – | – |
Topics
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("tigre")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btr057, 10.1073/pnas.0914285107, 10.1093/bioinformatics/btn278.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.