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CaDrA

Bioc current

Candidate Driver Analysis

v1.10.0 · software · GPL-3 + file LICENSE
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.18 · Oct 25, 2023

Current · Requires R 4.6

1.0 In 6 of 49 releases 3.23

Description

Performs both stepwise and backward heuristic search for candidate (epi)genetic drivers based on a binary multi-omics dataset. CaDrA's main objective is to identify features which, together, are significantly skewed or enriched pertaining to a given vector of continuous scores (e.g. sample-specific scores representing a phenotypic readout of interest, such as protein expression, pathway activity, etc.), based on the union occurence (i.e. logical OR) of the events.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

50 9 exported

Complexity

5.8 avg / 24 max

Call network

50 nodes / 57 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →
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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

7,514

Files

93

Compiled share

13.8%

Has compiled src

Yes

Language breakdown

R 3,623 (48.2%)C/C++/src 1,040 (13.8%)Tests 1,184 (15.8%)Docs 1,112 (14.8%)Vignettes 555 (7.4%)

API

Exported functions

9

Internal functions

16

Testing & CI

Has tests

Yes

Test-to-code ratio

0.33

testthat edition

3

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

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

4.4.0

System requirements

–

C++ standard

–

License

GPL-3 + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

6

First release

2024-03-13

Latest release

2026-04-28

Avg cadence

181 days

Cold removal rate

–

Dep drift

1

LOC over versions

v3.18: 7,299 LOCv3.19: 7,299 LOCv3.20: 7,514 LOCv3.21: 7,514 LOCv3.22: 7,514 LOCv3.23: 7,514 LOC

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

Documentation
READMEYes · 525 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 67% structuredCode of conductNoContributing guideNo
Examples that run
100%
Documented parameters
98%
Return-value docs
100%
References docs
47%

Topics

Software › Technology › Microarray
Software › Technology › Sequencing › RNASeq
Software › AssayDomain › GeneExpression
Software
Software › StatisticalMethod › FeatureExtraction

People

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