getDEE2

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see getDEE2.

Programmatic access to the DEE2 RNA expression dataset


Bioconductor version: 3.14

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 "4.1") 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 1.4.0
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
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_1.4.0.tar.gz
Windows Binary getDEE2_1.4.0.zip
macOS 10.13 (High Sierra) getDEE2_1.4.0.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 3.14 Source Archive