Package: DeeDeeExperiment 1.3.0

Najla Abassi

DeeDeeExperiment: DeeDeeExperiment: An S4 Class for managing and exploring omics analysis results

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.

Authors:Najla Abassi [aut, cre], Lea Schwarz [aut], Federico Marini [aut]

DeeDeeExperiment_1.3.0.tar.gz
DeeDeeExperiment_1.3.0.zip(r-4.7)DeeDeeExperiment_1.3.0.zip(r-4.6)DeeDeeExperiment_1.3.0.zip(r-4.5)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DeeDeeExperiment/json (API)

# Install 'DeeDeeExperiment' in R:
install.packages('DeeDeeExperiment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/imbeimainz/deedeeexperiment/issues

Datasets:

On BioConductor:DeeDeeExperiment-1.3.0(bioc 3.24)DeeDeeExperiment-1.2.0(bioc 3.23)

softwareinfrastructuredatarepresentationgeneexpressiontranscriptiontranscriptomicsdifferentialexpressionpathwaysgo

5.45 score 1 scripts 178 downloads 24 exports 51 dependencies

Last updated from:9bf542794e. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE324
linux-devel-x86_64OK501
source / vignettesOK534
linux-release-x86_64OK550
macos-release-arm64OK293
macos-oldrel-arm64OK375
windows-develOK463
windows-releaseOK602
windows-oldrelOK334
wasm-releaseOK290

Exports:addDEAaddFEAaddScenarioInfoDeeDeeExperimentexport_result_for_ddegetDEAgetDEAInfogetDEAInfo<-getDEAListgetDEANamesgetFEAgetFEAInfogetFEAInfo<-getFEAListgetFEANameslimma_list_for_ddelinkDEAandFEAmuscat_list_for_dderemoveDEAremoveFEArenameDEArenameFEAshowsupported_fea_formats

Dependencies:abindBHBiobaseBiocGenericsBiocParallelclicodetoolscpp11DelayedArrayDESeq2edgeRfarverformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtableIRangesisobandlabelinglambda.rlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsR6RColorBrewerRcppRcppArmadillorlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentsnowSparseArraystatmodSummarizedExperimentvctrsviridisLitewithrwritexlXVector

The DeeDeeExperiment User's Guide
Introduction | Why do we need a new class? | Anatomy of DeeDeeExperiment | Creating a DeeDeeExperiment object | Getting started | DeeDeeExperiment on the macrophage dataset | DEA: DESeq2 framework | DEA: limma framework | DEA: edgeR framework | Creating DeeDeeExperiment the DeeDee way | Adding results to a dde object | Adding DEA results | Adding multi-contrast DEA results | Adding FEA results | Linking DE and FE Analysis in a dde object | Adding contextual information | Summary of a dde object | Renaming results in a dde object | Removing results in a dde object | Accessing results stored in a dde object | Downstream operations with DeeDeeExperiment objects | FAQs | Session info | References
Rendered fromDeeDeeExperiment_manual.Rmdusingknitr::rmarkdown

Last update: 2026-03-09
Started: 2025-03-14

How to use DeeDeeExperiment with single-cell data
Differential State (DS) analysis with muscat & DeeDeeExperiment | DeeDeeExperiment on the Kang dataset | Session info | References
Rendered fromdde_with_single_cell.Rmdusingknitr::rmarkdown

Last update: 2025-12-05
Started: 2025-12-05

Readme and manuals

Help Manual

Help pageTopics
'clusterPro_res'clusterPro_res
dd_list_originaldd_list_original
A sample 'MArrayLM' objectde_limma
de_named_listde_named_list
The DeeDeeExperiment class.DeeDeeExperiment DeeDeeExperiment DeeDeeExperiment-class
Methods for DeeDeeExperiment objectsaddDEA addDEA,DeeDeeExperiment-method addFEA addFEA,DeeDeeExperiment-method addScenarioInfo addScenarioInfo,DeeDeeExperiment-method DeeDeeExperiment-methods getDEA getDEA,DeeDeeExperiment-method getDEAInfo getDEAInfo,DeeDeeExperiment-method getDEAInfo<- getDEAInfo<-,DeeDeeExperiment-method getDEAList getDEAList,DeeDeeExperiment-method getDEANames getDEANames,DeeDeeExperiment-method getFEA getFEA,DeeDeeExperiment-method getFEAInfo getFEAInfo,DeeDeeExperiment-method getFEAInfo<- getFEAInfo<-,DeeDeeExperiment-method getFEAList getFEAList,DeeDeeExperiment-method getFEANames getFEANames,DeeDeeExperiment-method linkDEAandFEA linkDEAandFEA,DeeDeeExperiment-method removeDEA removeDEA,DeeDeeExperiment-method removeFEA removeFEA,DeeDeeExperiment-method renameDEA renameDEA,DeeDeeExperiment-method renameFEA renameFEA,DeeDeeExperiment-method
Miscellaneous DeeDeeExperiment methodsDeeDeeExperiment-misc show,DeeDeeExperiment-method summary,DeeDeeExperiment-method
DeeDeeExperimentDeeDeeExperiment-package DeeDeeExperiment-pkg
A sample 'DGEExact' objectdge_exact_IFNg_both
A sample 'DGEExact' objectdge_exact_IFNg_naive
A sample 'DGEExact' objectdge_exact_Salm_both
A sample 'DGEExact' objectdge_exact_Salm_naive
A sample 'DGELRT' objectdge_lrt_IFNg_both
A sample 'DGELRT' objectdge_lrt_IFNg_naive
A sample 'DGELRT' objectdge_lrt_Salm_both
A sample 'DGELRT' objectdge_lrt_Salm_naive
'enrichr_res'enrichr_res
Export DEA/FEA/ASSAY results from a 'DeeDeeExperiment' to excel filesexport_result_for_dde
'fgseaRes'fgseaRes
'gost_res'gost_res
'gsea_res'gsea_res
A sample 'DESeqResults' objectIFNg_both
A sample 'DESeqResults' objectIFNg_naive
Convert a 'MArrayLM' object with multiple contrasts into a list of DE results tables compatible with DeeDeeExperimentlimma_list_for_dde
Convert 'muscat::pbDS()' results into a flat list of data frames compatible with 'DeeDeeExperiment'muscat_list_for_dde
'muscat_res'muscat_res
A sample 'DESeqResults' objectSalm_both
A sample 'DESeqResults' objectSalm_naive
Display available FEA formatssupported_fea_formats
'topGO_results_list'topGO_results_list