recount3

DOI: 10.18129/B9.bioc.recount3  

Explore and download data from the recount3 project

Bioconductor version: Release (3.16)

The recount3 package enables access to a large amount of uniformly processed RNA-seq data from human and mouse. You can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level with sample metadata and QC statistics. In addition we provide access to sample coverage BigWig files.

Author: Leonardo Collado-Torres [aut, cre]

Maintainer: Leonardo Collado-Torres <lcolladotor 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("recount3")

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("recount3")

 

HTML	R Script	recount3 quick start guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	Coverage, DataImport, DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	Artistic-2.0
Depends	SummarizedExperiment
Imports	BiocFileCache, methods, rtracklayer, S4Vectors, utils, RCurl, data.table, R.utils, Matrix, GenomicRanges, sessioninfo, tools
LinkingTo
Suggests	BiocStyle, covr, knitcitations, knitr, RefManageR, rmarkdown, testthat, pryr, interactiveDisplayBase, recount
SystemRequirements
Enhances
URL	https://github.com/LieberInstitute/recount3
BugReports	https://github.com/LieberInstitute/recount3/issues
Depends On Me
Imports Me
Suggests Me	RNAseqQC
Links To Me
Build Report

Package Archives

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

Source Package	recount3_1.8.0.tar.gz
Windows Binary	recount3_1.8.0.zip
macOS Binary (x86_64)	recount3_1.8.0.tgz
macOS Binary (arm64)	recount3_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/recount3
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/recount3
Bioc Package Browser	https://code.bioconductor.org/browse/recount3/
Package Short Url	https://bioconductor.org/packages/recount3/
Package Downloads Report	Download Stats