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 | 335 |
| Source branch | RELEASE_3_23 |
| biocViews | DataRepresentation, DifferentialExpression, GO, GeneExpression, Infrastructure, Pathways, Software, Transcription, Transcriptomics |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | DeeDeeExperiment_1.2.0.tar.gz |
| Windows binary (x86_64) | DeeDeeExperiment_1.2.0.zip |
| macOS binary (arm64) | DeeDeeExperiment_1.2.0.tgz |
| macOS binary (x86_64) | DeeDeeExperiment_1.2.0.tgz |
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)