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getDEE2

Programmatic access to the DEE2 RNA expression dataset


Bioconductor version: Release (3.18)

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 Ziemann <mark.ziemann at gmail.com>

Citation (from within R, enter citation("getDEE2")):

Installation

To install this package, start R (version "4.3") 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 PDF
NEWS Text

Details

biocViews GeneExpression, Sequencing, Software, Transcriptomics
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3
Depends R (>= 4.0)
Imports stats, utils, SummarizedExperiment, htm2txt
System Requirements
URL https://github.com/markziemann/getDEE2
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Suggests knitr, testthat, rmarkdown
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package getDEE2_1.12.0.tar.gz
Windows Binary getDEE2_1.12.0.zip (64-bit only)
macOS Binary (x86_64) getDEE2_1.12.0.tgz
macOS Binary (arm64) getDEE2_1.12.0.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/
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