getDEE2

DOI: 10.18129/B9.bioc.getDEE2  

Programmatic access to the DEE2 RNA expression dataset

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	getDEE2
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, Sequencing, Software, Transcriptomics
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	GPL-3
Depends	R (>= 4.0)
Imports	stats, utils, SummarizedExperiment, htm2txt
LinkingTo
Suggests	knitr, testthat, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/markziemann/getDEE2
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	getDEE2_1.8.0.tar.gz
Windows Binary	getDEE2_1.8.0.zip
macOS Binary (x86_64)	getDEE2_1.8.0.tgz
macOS Binary (arm64)	getDEE2_1.8.0.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
Old Source Packages for BioC 3.16	Source Archive