ideal
Bioc currentInteractive Differential Expression AnaLysis
Release Lineage
Entered 3.5 · Apr 25, 2017
Current · Requires R 4.6
Description
This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package. Support for reproducibility of the whole analysis is provided by means of a template report which gets automatically compiled and can be stored/shared.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
20 11 exported
Complexity
13.3 avg / 224 max
Call network
20 nodes / 9 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
7,841
Files
73
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
11
Internal functions
9
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
25%
Unsafe pattern score
57
Dep constraint coverage
7.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
19
First release
2017-04-24
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
12
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 13includes a package overview page
- Examples that run
- 83%10 run in a plain check · 1 never run · 1 hold no code
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- ideal User's Guide HTML
Repository practices
7 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/federicomarini/ideal on 2026-10-25.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2025-05-02 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| design_commas | data.frame | 8 × 10 | No other package |
| design_semicolons | data.frame | 8 × 10 | No other package |
| design_spaces | data.frame | 8 × 10 | No other package |
| design_tabs | data.frame | 8 × 10 | No other package |
| intro_countsoverview | – | – | – |
| intro_datasetup | – | – | – |
| intro_firsttour | – | – | – |
| intro_funcanalysis | – | – | – |
| intro_genefinder | – | – | – |
| intro_plots | – | – | – |
| intro_report | data.frame | 1 × 2 | No other package |
| intro_results | – | – | – |
| intro_signatureexplorer | – | – | – |
Topics
People
- Federico Marini author maintainer
Cite
Cite this package
Run in R for the authors' entry:
citation("ideal")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s12859-020-03819-5, 10.1002/cpz1.411.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.