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DeeDeeExperiment

This is the development version of DeeDeeExperiment; to use it, please install the devel version of Bioconductor.

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


Bioconductor version: Development (3.22)

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.

Author: Najla Abassi [aut, cre] ORCID iD ORCID: 0000-0001-8357-0938 , Lea Rothörl [aut] ORCID iD ORCID: 0000-0003-2554-0583 , Federico Marini [aut] ORCID iD ORCID: 0000-0003-3252-7758

Maintainer: Najla Abassi <abassi.nejla96 at gmail.com>

Citation (from within R, enter citation("DeeDeeExperiment")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("DeeDeeExperiment")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DeeDeeExperiment")
The DeeDeeExperiment User's Guide HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DataRepresentation, DifferentialExpression, GO, GeneExpression, Infrastructure, Pathways, Software, Transcription, Transcriptomics
Version 0.99.5
In Bioconductor since BioC 3.22 (R-4.5)
License MIT + file LICENSE
Depends R (>= 4.5.0), SingleCellExperiment
Imports SummarizedExperiment, methods, S4Vectors, utils, DESeq2, edgeR, limma, cli
System Requirements
URL https://github.com/imbeimainz/DeeDeeExperiment
Bug Reports https://github.com/imbeimainz/DeeDeeExperiment/issues
See More
Suggests macrophage, knitr, BiocStyle, apeglm, mosdef, org.Hs.eg.db, topGO, clusterProfiler, DEFormats, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DeeDeeExperiment_0.99.5.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64) DeeDeeExperiment_0.99.5.tgz
macOS Binary (arm64) DeeDeeExperiment_0.99.5.tgz
Source Repository git clone https://git.bioconductor.org/packages/DeeDeeExperiment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DeeDeeExperiment
Bioc Package Browser https://code.bioconductor.org/browse/DeeDeeExperiment/
Package Short Url https://bioconductor.org/packages/DeeDeeExperiment/
Package Downloads Report Download Stats