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 (3.21)

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

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

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DataImport, DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version	1.33.0
In Bioconductor since	BioC 3.4 (R-3.3) (8 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/

Suggests	AnnotationDbi, BiocManager, BiocStyle(>= 2.5.19), DESeq2, sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures, txdbmaker, 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
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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