SVMDO
Bioc currentIdentification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by Disease Ontology
Release Lineage
Entered 3.17 · Apr 26, 2023
Current · Requires R 4.6
Description
It is an easy-to-use GUI using disease information for detecting tumor/normal sample discriminating gene sets from differentially expressed genes. Our approach is based on an iterative algorithm filtering genes with disease ontology enrichment analysis and wilk and wilks lambda criterion connected to SVM classification model construction. Along with gene set extraction, SVMDO also provides individual prognostic marker detection. The algorithm is designed for FPKM and RPKM normalized RNA-Seq transcriptome datasets.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
42 1 exported
Complexity
2.6 avg / 15 max
Call network
42 nodes / 20 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
3,310
Files
102
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
1
Internal functions
41
Testing & CI
Has tests
Yes
Test-to-code ratio
0.34
testthat edition
3
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
82.6%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
7
First release
2023-04-25
Latest release
2026-04-28
Avg cadence
189 days
Cold removal rate
–
Dep drift
1
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
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Mustafa Erhan Ozer author maintainer
- Kazim Yalcin Arga author
- Pemra Ozbek Sarica author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("SVMDO")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.