recount

DOI: 10.18129/B9.bioc.recount  

Explore and download data from the recount project

Bioconductor version: Release (3.16)

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 [aut, cre] , Abhinav Nellore [ctb], Andrew E. Jaffe [ctb] , Margaret A. Taub [ctb], Kai Kammers [ctb], Shannon E. Ellis [ctb] , Kasper Daniel Hansen [ctb] , Ben Langmead [ctb] , Jeffrey T. Leek [aut, ths]

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("recount")

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("recount")

 

HTML	R Script	Basic DESeq2 results exploration
HTML	R Script	recount quick start guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	Coverage, DataImport, DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version	1.24.1
In Bioconductor since	BioC 3.4 (R-3.3) (6.5 years)
License	Artistic-2.0
Depends	R (>= 3.5.0), 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, RnaSeqSampleSize
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	recount_1.24.1.tar.gz
Windows Binary	recount_1.24.1.zip
macOS Binary (x86_64)	recount_1.24.1.tgz
macOS Binary (arm64)	recount_1.24.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/recount
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/recount
Bioc Package Browser	https://code.bioconductor.org/browse/recount/
Package Short Url	https://bioconductor.org/packages/recount/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive