recount

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see recount.

Explore and download data from the recount project


Bioconductor version: 3.10

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>

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

Installation

To install this package, start R (version "3.6") 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")
Basic DESeq2 results exploration HTML R Script
recount quick start guide HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, DataImport, DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.12.1
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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
System Requirements
URL https://github.com/leekgroup/recount
Bug Reports https://support.bioconductor.org/t/recount/
See More
Suggests AnnotationDbi, BiocManager, BiocStyle(>= 2.5.19), DESeq2, sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures, knitcitations, knitr (>= 1.6), org.Hs.eg.db, RefManageR, regionReport(>= 1.9.4), rmarkdown (>= 0.9.5), testthat (>= 2.1.0)
Linking To
Enhances
Depends On Me
Imports Me psichomics, recountWorkflow
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package recount_1.12.1.tar.gz
Windows Binary recount_1.12.1.zip
Mac OS X 10.11 (El Capitan) recount_1.12.1.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 3.10 Source Archive