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)
#> 
#> Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD,
#> Jaffe AE, Langmead B, Leek JT (2017). "Reproducible RNA-seq analysis
#> using recount2." _Nature Biotechnology_. doi: 10.1038/nbt.3838 (URL:
#> https://doi.org/10.1038/nbt.3838), <URL:
#> http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {Reproducible RNA-seq analysis using recount2},
#>     author = {Leonardo Collado-Torres and Abhinav Nellore and Kai Kammers and Shannon E. Ellis and Margaret A. Taub and Kasper D. Hansen and Andrew E. Jaffe and Ben Langmead and Jeffrey T. Leek},
#>     year = {2017},
#>     journal = {Nature Biotechnology},
#>     doi = {10.1038/nbt.3838},
#>     url = {http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html},
#>   }
#> 
#> Collado-Torres L, Nellore A, Jaffe AE (2017). "recount workflow:
#> Accessing over 70,000 human RNA-seq samples with Bioconductor [version
#> 1; referees: 1 approved, 2 approved with reservations]."
#> _F1000Research_. doi: 10.12688/f1000research.12223.1 (URL:
#> https://doi.org/10.12688/f1000research.12223.1), <URL:
#> https://f1000research.com/articles/6-1558/v1>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor [version 1; referees: 1 approved, 2 approved with reservations]},
#>     author = {Leonardo Collado-Torres and Abhinav Nellore and Andrew E. Jaffe},
#>     year = {2017},
#>     journal = {F1000Research},
#>     doi = {10.12688/f1000research.12223.1},
#>     url = {https://f1000research.com/articles/6-1558/v1},
#>   }
#> 
#> Ellis SE, Collado-Torres L, Jaffe AE, Leek JT (2018). "Improving the
#> value of public RNA-seq expression data by phenotype prediction."
#> _Nucl. Acids Res._. doi: 10.1093/nar/gky102 (URL:
#> https://doi.org/10.1093/nar/gky102), <URL:
#> https://doi.org/10.1093/nar/gky102>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {Improving the value of public RNA-seq expression data by phenotype prediction},
#>     author = {Shannon E. Ellis and Leonardo Collado-Torres and Andrew E. Jaffe and Jeffrey T. Leek},
#>     year = {2018},
#>     journal = {Nucl. Acids Res.},
#>     doi = {10.1093/nar/gky102},
#>     url = {https://doi.org/10.1093/nar/gky102},
#>   }
#> 
#> Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD,
#> Jaffe AE, Langmead B, Leek JT (2020). _Explore and download data from
#> the recount project_. doi: 10.18129/B9.bioc.recount (URL:
#> https://doi.org/10.18129/B9.bioc.recount),
#> https://github.com/leekgroup/recount - R package version 1.17.1, <URL:
#> http://www.bioconductor.org/packages/recount>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {Explore and download data from the recount project},
#>     author = {Leonardo Collado-Torres and Abhinav Nellore and Kai Kammers and Shannon E. Ellis and Margaret A. Taub and Kasper D. Hansen and Andrew E. Jaffe and Ben Langmead and Jeffrey T. Leek},
#>     year = {2020},
#>     url = {http://www.bioconductor.org/packages/recount},
#>     note = {https://github.com/leekgroup/recount - R package version 1.17.1},
#>     doi = {10.18129/B9.bioc.recount},
#>   }
#> 
#> Frazee AC, Langmead B, Leek JT (2011). "ReCount: A multi-experiment
#> resource of analysis-ready RNA-seq gene count datasets." _BMC
#> Bioinformatics_. doi: 10.1186/1471-2105-12-449 (URL:
#> https://doi.org/10.1186/1471-2105-12-449), <URL:
#> https://doi.org/10.1186/1471-2105-12-449>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets},
#>     author = {Alyssa C. Frazee and Ben Langmead and Jeffrey T. Leek},
#>     year = {2011},
#>     journal = {BMC Bioinformatics},
#>     doi = {10.1186/1471-2105-12-449},
#>     url = {https://doi.org/10.1186/1471-2105-12-449},
#>   }
#> 
#> Razmara A, Ellis SE, Sokolowski DJ, Davis S, Wilson MD, Leek JT, Jaffe
#> AE, Collado-Torres L (2019). "recount-brain: a curated repository of
#> human brain RNA-seq datasets metadata." _bioRxiv_. doi: 10.1101/618025
#> (URL: https://doi.org/10.1101/618025), <URL:
#> https://doi.org/10.1101/618025>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {recount-brain: a curated repository of human brain RNA-seq datasets metadata},
#>     author = {Ashkaun Razmara and Shannon E. Ellis and Dustin J. Sokolowski and Sean Davis and Michael D. Wilson and Jeffrey T. Leek and Andrew E. Jaffe and Leonardo Collado-Torres},
#>     year = {2019},
#>     journal = {bioRxiv},
#>     doi = {10.1101/618025},
#>     url = {https://doi.org/10.1101/618025},
#>   }
#> 
#> Imada E, Sanchez DF, Collado-Torres L, Wilks C, Matam T, Dinalankara W,
#> Stupnikov A, Lobo-Pereira F, Yip C, Yasuzawa K, Kondo N, Itoh M, Suzuki
#> H, Kasukawa T, Hon CC, de Hoon MJ, Shin JW, Carninci P, Jaffe AE, Leek
#> JT, Favorov A, Franco GR, Langmead B, Marchionni L (2020). "Recounting
#> the FANTOM CAGE–Associated Transcriptome." _Genome Research_. doi:
#> 10.1101/gr.254656.119 (URL: https://doi.org/10.1101/gr.254656.119),
#> <URL: https://doi.org/10.1101/gr.254656.119>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {Recounting the FANTOM CAGE–Associated Transcriptome},
#>     author = {Eddie-Luidy Imada and Diego Fernando Sanchez and Leonardo Collado-Torres and Christopher Wilks and Tejasvi Matam and Wikum Dinalankara and Aleksey Stupnikov and Francisco Lobo-Pereira and Chi-Wai Yip and Kayoko Yasuzawa and Naoto Kondo and Masayoshi Itoh and Harukazu Suzuki and Takeya Kasukawa and Chung Chau Hon and Michiel JL {de Hoon} and Jay W Shin and Piero Carninci and Andrew E. Jaffe and Jeffrey T. Leek and Alexander Favorov and Glória R Franco and Ben Langmead and Luigi Marchionni},
#>     year = {2020},
#>     journal = {Genome Research},
#>     doi = {10.1101/gr.254656.119},
#>     url = {https://doi.org/10.1101/gr.254656.119},
#>   }

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 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.