recount: Explore and download data from the recount project

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.

Package details

AuthorLeonardo Collado-Torres [aut, cre] (<https://orcid.org/0000-0003-2140-308X>), Abhinav Nellore [ctb], Andrew E. Jaffe [ctb] (<https://orcid.org/0000-0001-6886-1454>), Margaret A. Taub [ctb], Kai Kammers [ctb], Shannon E. Ellis [ctb] (<https://orcid.org/0000-0002-9231-0481>), Kasper Daniel Hansen [ctb] (<https://orcid.org/0000-0003-0086-0687>), Ben Langmead [ctb] (<https://orcid.org/0000-0003-2437-1976>), Jeffrey T. Leek [aut, ths] (<https://orcid.org/0000-0002-2873-2671>)
Bioconductor views Coverage DataImport DifferentialExpression GeneExpression ImmunoOncology RNASeq Sequencing Software
MaintainerLeonardo Collado-Torres <lcolladotor@gmail.com>
LicenseArtistic-2.0
Version1.16.1
URL https://github.com/leekgroup/recount
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("recount")

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recount documentation built on Dec. 20, 2020, 2:01 a.m.