bnem
Bioc currentTraining of logical models from indirect measurements of perturbation experiments
Release Lineage
Entered 3.13 · May 20, 2021
Current · Requires R 4.6
Description
bnem combines the use of indirect measurements of Nested Effects Models (package mnem) with the Boolean networks of CellNOptR. Perturbation experiments of signalling nodes in cells are analysed for their effect on the global gene expression profile. Those profiles give evidence for the Boolean regulation of down-stream nodes in the network, e.g., whether two parents activate their child independently (OR-gate) or jointly (AND-gate).
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
59 19 exported
Complexity
14.2 avg / 103 max
Call network
59 nodes / 72 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
9,285
Files
39
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
19
Internal functions
5
Testing & CI
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
CI present
No
CI type
[]
PR gated
No
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
4.1
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
11
First release
2021-05-19
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
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
- 97%
- Return-value docs
- 100%
- References docs
- 4%
Topics
People
- Martin Pirkl author maintainer