README.md
In recount3: Explore and download data from the recount3 project

recount3

The 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.

For more information about recount3 check the vignettes through Bioconductor or at the documentation website.

Get the latest stable R release from CRAN. Then install recount3 using from Bioconductor the following code:

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

BiocManager::install("recount3")

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)
#> 
#> Collado-Torres L (2020). _Explore and download data from the recount3
#> project_. doi: 10.18129/B9.bioc.recount3 (URL:
#> https://doi.org/10.18129/B9.bioc.recount3),
#> https://github.com/LieberInstitute/recount3 - R package version 0.99.5,
#> <URL: http://www.bioconductor.org/packages/recount3>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {Explore and download data from the recount3 project},
#>     author = {Leonardo Collado-Torres},
#>     year = {2020},
#>     url = {http://www.bioconductor.org/packages/recount3},
#>     note = {https://github.com/LieberInstitute/recount3 - R package version 0.99.5},
#>     doi = {10.18129/B9.bioc.recount3},
#>   }
#> 
#> Wilks C, Collado-Torres L, Zheng SC, Jaffe AE, Nellore A, Hansen KD,
#> Langmead B (2020). "recount3 pre-print title TODO." _bioRxiv_. doi:
#> 10.1101/TODO (URL: https://doi.org/10.1101/TODO), <URL:
#> https://www.biorxiv.org/content/10.1101/TODO>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {recount3 pre-print title TODO},
#>     author = {Christopher Wilks and Leonardo Collado-Torres and Shijie C. Zheng and Andrew E. Jaffe and Abhinav Nellore and Kasper D. Hansen and Ben Langmead},
#>     year = {2020},
#>     journal = {bioRxiv},
#>     doi = {10.1101/TODO},
#>     url = {https://www.biorxiv.org/content/10.1101/TODO},
#>   }

Please note that 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.

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.

Continuous code testing is possible thanks to GitHub actions through usethis, remotes, sysreqs and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
Code coverage assessment is possible thanks to codecov and covr.
The documentation website is automatically updated thanks to pkgdown.
The code is styled automatically thanks to styler.
The documentation is formatted thanks to devtools and roxygen2.

For more details, check the dev directory.

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 | recount | | 2020 | recount3 | DOI: TODO | recount3 |

The ReCount family involves the following teams:

| | | | | | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------- | | | | | |