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")):Mark Ziemann, Antony Kaspi. getDEE2: Programmatic access to the DEE2 RNA expression dataset. doi:10.18129/B9.bioc.getDEE2, R package version 1.22.0, https://bioconductor.org/packages/getDEE2.
Generated from the package metadata; it may differ from the package's own citation.
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, r-universe |
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 |
| Package Short Url | https://bioconductor.org/packages/getDEE2/ |
| Package Downloads Report | Download Stats |