progeny
Bioc currentPathway RespOnsive GENes for activity inference from gene expression
Release Lineage
Entered 3.6 · Oct 31, 2017
Current · Requires R 4.6
Description
PROGENy is resource that leverages a large compendium of publicly available signaling perturbation experiments to yield a common core of pathway responsive genes for human and mouse. These, coupled with any statistical method, can be used to infer pathway activities from bulk or single-cell transcriptomics.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
10 5 exported
Complexity
4.4 avg / 16 max
Call network
10 nodes / 5 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
1,133
Files
71
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
5
Internal functions
5
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.06
testthat edition
–
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
3.6.0
System requirements
–
C++ standard
–
License
Apache License (== 2.0) | file LICENSE
License flags
not SPDX, not OSI
History
Versions
18
First release
2017-10-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
8
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 8includes a package overview page
- Examples that run
- 100%8 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
2 development-tooling and community-health practices detected across 1 family in the upstream repository
Checks run against github.com/saezlab/progeny on 2026-10-21.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| human_def_expected | data.frame | 8 × 15 | No other package |
| human_input | data.frame | 121 × 9 | No other package |
| human_perm_expected | data.frame | 8 × 15 | No other package |
| model_human_full | data.frame | 274,143 × 4 | No other package |
| model_mouse_full | data.frame | 219,067 × 4 | No other package |
| mouse_def_expected | data.frame | 8 × 15 | No other package |
| mouse_input | data.frame | 88 × 9 | No other package |
| mouse_perm_expected | data.frame | 8 × 15 | No other package |
| vignette_data | list | 3 elements | 2 packages |
Topics
Depended on by (1)
Bioconductor (1)
Suggested by (1)
People
- Aurélien Dugourd maintainer contributor
- Igor Bulanov contributor
- Christian H. Holland contributor
- Michael Schubert author
- Alberto Valdeolivas contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("progeny")The package provides a citation file, so citation() returns the authors' own entry.
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.