oligo
Bioc currentPreprocessing tools for oligonucleotide arrays
Release Lineage
Entered 1.6 · May 18, 2005
Current · Requires R 4.6
Description
A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
203 30 exported
Complexity
5 avg / 31 max
Call network
203 nodes / 266 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
12,101
Files
113
Compiled share
16.9%
Has compiled src
Yes
Language breakdown
API
Exported functions
33
Internal functions
129
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
93.9%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
3.6%
Unsafe pattern score
0
Dep constraint coverage
52.9%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.2.0
System requirements
–
C++ standard
–
License
LGPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
43
First release
2005-05-19
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
29
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 43includes a package overview page
- Examples that run
- 75%15 run in a plain check · 4 never run · 1 hold no code
- Exported functions with examples
- 57%
- Documented parameters
- 99%
- Return-value docs
- 86%
- Help pages citing references
- 12%
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/benilton/oligo on 2026-10-22.
Topics
Depended on by (185)
Show 43 packagesHide 43 packages
Bioconductor (185)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("oligo")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btq431.
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.