recount

DOI: 10.18129/B9.bioc.recount    

This is the development version of recount; for the stable release version, see recount.

Explore and download data from the recount project

Bioconductor version: Development (3.15)

Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.

Author: Leonardo Collado-Torres <lcolladotor at gmail.com>, Abhinav Nellore <anellore at gmail.com>, Andrew Jaffe <andrew.jaffe at libd.org>, E. Taub <mtaub at jhsph.edu>, Margaret Kammers <kai.kammers at gmail.com>, A. Ellis <sellis18 at jhmi.edu>, Kai Hansen <kasperdanielhansen at gmail.com>, Shannon Langmead <langmea at cs.jhu.edu>, E. Leek <jtleek at gmail.com>, Kasper Collado-Torres <lcolladotor at gmail.com>, Daniel Nellore <anellore at gmail.com>, Ben Jaffe <andrew.jaffe at libd.org>, Jeffrey Taub <mtaub at jhsph.edu>, T. Kammers <kai.kammers at gmail.com>

Maintainer: Leonardo Collado-Torres <lcolladotor at gmail.com>

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

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("recount")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews Coverage, DataImport, DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.21.0
In Bioconductor since BioC 3.4 (R-3.3) (5 years)
License Artistic-2.0
Depends R (>= 3.3.0), SummarizedExperiment
Imports BiocParallel, derfinder, downloader, GEOquery, GenomeInfoDb, GenomicRanges, IRanges, methods, RCurl, rentrez, rtracklayer(>= 1.35.3), S4Vectors, stats, utils
LinkingTo
Suggests AnnotationDbi, BiocManager, BiocStyle(>= 2.5.19), DESeq2, sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures, knitr (>= 1.6), org.Hs.eg.db, RefManageR, regionReport(>= 1.9.4), rmarkdown (>= 0.9.5), testthat (>= 2.1.0), covr, pheatmap, DT, edgeR, ggplot2, RColorBrewer
SystemRequirements
Enhances
URL https://github.com/leekgroup/recount
BugReports https://support.bioconductor.org/t/recount/
Depends On Me
Imports Me psichomics, recountWorkflow, RNAAgeCalc
Suggests Me dasper, ODER, recount3
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/recount
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/recount
Package Short Url https://bioconductor.org/packages/recount/
Package Downloads Report Download Stats

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