DeeDeeExperiment

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

Bioconductor version: 3.23 · Package version: 1.2.0

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.

Installation

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

BiocManager::install("DeeDeeExperiment")

Details

Maintainer	Najla Abassi <abassi.nejla96@gmail.com>
Author	Najla Abassi [aut, cre] (ORCID: <https://orcid.org/0000-0001-8357-0938>), Lea Schwarz [aut] (ORCID: <https://orcid.org/0000-0003-2554-0583>), Federico Marini [aut] (ORCID: <https://orcid.org/0000-0003-3252-7758>)
License	MIT + file LICENSE
URL	https://github.com/imbeimainz/DeeDeeExperiment
Bug Reports	https://github.com/imbeimainz/DeeDeeExperiment/issues
Downloads rank	150
Source branch	RELEASE_3_23
biocViews	DataRepresentation, DifferentialExpression, GO, GeneExpression, Infrastructure, Pathways, Software, Transcription, Transcriptomics

Documentation

Download

Source package

Dependencies

Depends: R (>= 4.5.0), SingleCellExperiment

Imports: SummarizedExperiment, methods, S4Vectors, utils, DESeq2, edgeR, limma, writexl, cli

Suggests: macrophage, knitr, BiocStyle, apeglm, mosdef, org.Hs.eg.db, topGO, clusterProfiler, DEFormats, ExperimentHub, scater, muscat, testthat (>= 3.0.0)