DeeDeeExperiment
This is the development version of DeeDeeExperiment; for the stable release version, see DeeDeeExperiment.
DeeDeeExperiment: An S4 Class for managing and exploring omics analysis results
Bioconductor version: Development (3.24)
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]
, Lea Schwarz [aut]
, Federico Marini [aut]
Maintainer: Najla Abassi <abassi.nejla96 at gmail.com>
citation("DeeDeeExperiment")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| 1. The DeeDeeExperiment User's Guide | HTML | R Script |
| 2. How to use DeeDeeExperiment with single-cell data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataRepresentation, DifferentialExpression, GO, GeneExpression, Infrastructure, Pathways, Software, Transcription, Transcriptomics |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0), SingleCellExperiment |
| Imports | SummarizedExperiment, methods, S4Vectors, utils, DESeq2, edgeR, limma, writexl, 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, ExperimentHub, scater, muscat, 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_1.3.0.tar.gz |
| Windows Binary (x86_64) | DeeDeeExperiment_1.3.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | DeeDeeExperiment_1.3.0.tgz |
| macOS Binary (sonoma-arm64) | DeeDeeExperiment_1.3.0.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 |