ASSIGN
Bioc currentAdaptive Signature Selection and InteGratioN (ASSIGN)
Release Lineage
Entered 2.14 · Apr 14, 2014
Current · Requires R 4.6
Description
ASSIGN is a computational tool to evaluate the pathway deregulation/activation status in individual patient samples. ASSIGN employs a flexible Bayesian factor analysis approach that adapts predetermined pathway signatures derived either from knowledge-based literature or from perturbation experiments to the cell-/tissue-specific pathway signatures. The deregulation/activation level of each context-specific pathway is quantified to a score, which represents the extent to which a patient sample encompasses the pathway deregulation/activation signature.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
24 13 exported
Complexity
7.8 avg / 30 max
Call network
24 nodes / 27 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
4,197
Files
91
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
13
Internal functions
11
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.05
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.4
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
25
First release
2014-04-11
Latest release
2026-04-28
Avg cadence
183 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
- 18
- Examples that run
- 60%6 run in a plain check · 4 never run
- Exported functions with examples
- 77%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- Primer HTML
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/compbiomed/assign on 2026-10-18.
GitHub Pages site last deployed 2023-05-26
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| excludegenes | vector | 79 elements | No other package |
| geneList1 | list | 5 elements | No other package |
| gfrn_geneList | list | 18 elements | No other package |
| testData1 | data.frame | 1,000 × 111 | No other package |
| trainingData1 | data.frame | 1,000 × 55 | No other package |
Topics
Depended on by (1)
Bioconductor (1)
People
- David Jenkins author maintainer
- Andrea H. Bild author
- W. Evan Johnson author
- Mumtehena Rahman author
- Ying Shen author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("ASSIGN")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.