In leekgroup/recount: Explore and download data from the recount project

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)

recount

Explore and download data from the recount project available at the recount2 website. 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 derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project.

Documentation

For more information about recount check the vignettes through Bioconductor or at the documentation website.

Installation instructions

Get the latest stable R release from CRAN. Then install recount from Bioconductor using the following code:

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

BiocManager::install("recount")

Citation

Below is the citation output from using citation('recount') in R. Please run this yourself to check for any updates on how to cite recount.

print(citation("recount"), bibtex = TRUE)

Please note that the recount was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

Code of Conduct

Please note that the recount project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Development tools

Continuous code testing is possible thanks to GitHub actions through r BiocStyle::CRANpkg('usethis'), r BiocStyle::CRANpkg('remotes'), r BiocStyle::Githubpkg('r-hub/sysreqs') and r BiocStyle::CRANpkg('rcmdcheck') customized to use Bioconductor's docker containers and r BiocStyle::Biocpkg('BiocCheck').
Code coverage assessment is possible thanks to codecov and r BiocStyle::CRANpkg('covr').
The documentation website is automatically updated thanks to r BiocStyle::CRANpkg('pkgdown').
The code is styled automatically thanks to r BiocStyle::CRANpkg('styler').
The documentation is formatted thanks to r BiocStyle::CRANpkg('devtools') and r BiocStyle::CRANpkg('roxygen2').