DeeDeeExperiment
Bioc currentDeeDeeExperiment: An S4 Class for managing and exploring omics analysis results
Release Lineage
Entered 3.22 · Oct 30, 2025
Current · Requires R 4.6
Description
DeeDeeExperiment is an S4 class extending the SingleCellExperiment class, designed to integrate and manage omics analysis results. It introduces two dedicated slots to store Differential Expression Analysis (DEA) results and Functional Enrichment Analysis (FEA) results, providing a structured approach for downstream analysis.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
29 5 exported
Complexity
6.5 avg / 33 max
Call network
29 nodes / 26 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
8,212
Files
82
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
23
Internal functions
24
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.29
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
2
First release
2025-10-29
Latest release
2026-04-28
Avg cadence
181 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
- Help pages
- 30includes a package overview page
- Examples that run
- 100%6 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 43%
- The
deaandfeaslots now useS4Vectors::SimpleListinstead of baselist - The DEA original objects are no longer stored in the
deaslot. They are now
stored under metadata(dde)$singlecontrast or metadata(dde)$multicontrast, and
each contrast entry in the dea slot contains a pointer to its original object
- Added helper functions to simplify inserting DE results from
muscat::pbDS()
and MArrayLM object with multiple contrast into a dde object
- Added a helper function to export results stored in
deaandfeaslots as
excel files
- Improved warning messages
- A new vignette showcasing how to apply
DeeDeeExperimentto a single-cell
dataset
- Updating citation since the
DeeDeeExperimentpaper is out!
From NEWS.md in the release
Repository practices
6 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/imbeimainz/deedeeexperiment on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-07-24 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| IFNg_both | – | – | – |
| IFNg_naive | – | – | – |
| Salm_both | – | – | – |
| Salm_naive | – | – | – |
| anns | data.frame | 17,806 × 3 | No other package |
| clusterPro_res | list | 2 elements | No other package |
| david_output_chart_BPonly_ifng_vs_naive | data.frame | 237 × 13 | 2 packages |
| de_limma | MArrayLM | 22 elements | No other package |
| de_named_list | list | 4 elements | No other package |
| dge_exact_IFNg_both | DGEExact | 3 elements | No other package |
| dge_exact_IFNg_naive | DGEExact | 3 elements | No other package |
| dge_exact_Salm_both | DGEExact | 3 elements | No other package |
| dge_exact_Salm_naive | DGEExact | 3 elements | No other package |
| dge_lrt_IFNg_both | DGELRT | 18 elements | No other package |
| dge_lrt_IFNg_naive | DGELRT | 18 elements | No other package |
| dge_lrt_Salm_both | DGELRT | 18 elements | No other package |
| dge_lrt_Salm_naive | DGELRT | 18 elements | No other package |
| enrichr_res | list | 3 elements | No other package |
| fgseaRes | data.table | 4,576 × 8 | No other package |
| gost_res | list | 2 elements | No other package |
| gsea_res | – | – | – |
| muscat_res | list | 4 elements | No other package |
| topGO_results_list | list | 4 elements | No other package |
Topics
Depended on by (1)
Bioconductor (1)
People
- Najla Abassi author maintainer
- Federico Marini author
- Lea Schwarz author
Cite
Cite this package
Run in R for the authors' entry:
citation("DeeDeeExperiment")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btag157.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.