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DeeDeeExperiment
This is thereleased version of DeeDeeExperiment; for the devel version, seeDeeDeeExperiment.
DeeDeeExperiment: An S4 Class for managing and exploring omics analysis results
Bioconductor version: Release (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: 0000-0001-8357-0938, Lea Rothörl [aut] ORCID: 0000-0003-2554-0583, Federico Marini [aut] ORCID: 0000-0003-3252-7758
Maintainer: Najla Abassi <abassi.nejla96 at gmail.com>
citation("DeeDeeExperiment")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("DeeDeeExperiment")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataRepresentation,DifferentialExpression,GO,GeneExpression,Infrastructure,Pathways,Software,Transcription,Transcriptomics |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| License | MIT + fileLICENSE |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | DeeDeeExperiment_1.0.0.tar.gz |
| Windows Binary (x86_64) | DeeDeeExperiment_1.0.0.zip |
| macOS Binary (x86_64) | DeeDeeExperiment_1.0.0.tgz |
| macOS Binary (arm64) | DeeDeeExperiment_1.0.0.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 |