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recount3

Explore and download data from the recount3 project


Bioconductor version: Release (3.19)

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>

Citation (from within R, enter citation("recount3")):

Installation

To install this package, start R (version "4.4") 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")
recount3 quick start guide HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, DataImport, DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software
Version 1.14.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends SummarizedExperiment
Imports BiocFileCache, methods, rtracklayer, S4Vectors, utils, httr, data.table, R.utils, Matrix, GenomicRanges, sessioninfo, tools
System Requirements
URL https://github.com/LieberInstitute/recount3
Bug Reports https://github.com/LieberInstitute/recount3/issues
See More
Suggests BiocStyle, covr, knitcitations, knitr, RefManageR, rmarkdown, testthat, pryr, interactiveDisplayBase, recount
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me RNAseqQC
Links To Me
Build Report Build Report

Package Archives

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

Source Package recount3_1.14.0.tar.gz
Windows Binary recount3_1.14.0.zip (64-bit only)
macOS Binary (x86_64) recount3_1.14.0.tgz
macOS Binary (arm64) recount3_1.14.0.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