getDEE2
This is the released version of getDEE2; for the devel version, see getDEE2.
Programmatic access to the DEE2 RNA expression dataset
Bioconductor version: Release (3.23)
Digital Expression Explorer 2 (or DEE2 for short) is a repository of processed RNA-seq data in the form of counts. It was designed so that researchers could undertake re-analysis and meta-analysis of published RNA-seq studies quickly and easily. As of April 2020, over 1 million SRA datasets have been processed. This package provides an R interface to access these expression data. More information about the DEE2 project can be found at the project homepage (http://dee2.io) and main publication (https://doi.org/10.1093/gigascience/giz022).
Author: Mark Ziemann [aut, cre], Antony Kaspi [aut]
Maintainer: Mark 0000-0002-7688-6974 Ziemann <mark.ziemann at gmail.com>
citation("getDEE2")):
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")
BiocManager::install("getDEE2")
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("getDEE2")| getDEE2 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, Sequencing, Software, Transcriptomics |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | GPL-3 |
| Depends | R (>= 4.4) |
| Imports | stats, utils, SummarizedExperiment, htm2txt |
| System Requirements | |
| URL | https://github.com/markziemann/getDEE2 |
| Bug Reports | https://github.com/markziemann/getDEE2 |
See More
| Suggests | knitr, testthat, rmarkdown |
| 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 | getDEE2_1.22.0.tar.gz |
| Windows Binary (x86_64) | getDEE2_1.22.0.zip |
| macOS Binary (big-sur-x86_64) | getDEE2_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | getDEE2_1.22.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/getDEE2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/getDEE2 |
| Bioc Package Browser | https://code.bioconductor.org/browse/getDEE2/ |
| Package Short Url | https://bioconductor.org/packages/getDEE2/ |
| Package Downloads Report | Download Stats |