In LieberInstitute/recount3: Explore and download data from the recount3 project

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

recount3

The r Biocpkg('recount3') R/Bioconductor package is part of the recount3 project and is the latest iteration of the ReCount family of projects that provide access to uniformly-processed RNA sequencing datasets. The main documentation website for all the recount3-related projects is available at recount.bio. Please check that website for more information about how this R/Bioconductor package and other tools are related to each other.

Documentation

For more information about r Biocpkg('recount3') check the vignettes through Bioconductor or at the documentation website.

Installation instructions

Get the latest stable R release from CRAN. Then install r Biocpkg('recount3') from Bioconductor using the following code:

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

BiocManager::install("recount3")

Citation

Below is the citation output from using citation('recount3') in R. Please run this yourself to check for any updates on how to cite recount3.

print(citation("recount3"), bibtex = TRUE)

Please note that r Biocpkg('recount3') 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 derfinderPlot 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').

For more details, check the dev directory.

Project history

To clarify the relationship between the R/Bioconductor packages and the phases of ReCount please check the table below:

| Year | Phase | Main references | R/Bioconductor | | --- | --- | --- | --- | | 2011 | ReCount | DOI: 10.1186/1471-2105-12-449 | none | | 2017 | recount2 | DOI: 10.1038/nbt.3838 10.12688/f1000research.12223.1 | r Biocpkg('recount') | | 2021 | recount3 | DOI: 10.1186/s13059-021-02533-6 | r Biocpkg('recount3') |