recount
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20 hours ago •
leekgroup
leekgroup
R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/
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)
#> To cite package 'recount' in publications use:
#>
#> 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
#> <https://doi.org/10.1038/nbt.3838>,
#> <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
#> <https://doi.org/10.12688/f1000research.12223.1>,
#> <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
#> <https://doi.org/10.1093/nar/gky102>,
#> <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 (2023). _Explore and download data from
#> the recount project_. doi:10.18129/B9.bioc.recount
#> <https://doi.org/10.18129/B9.bioc.recount>,
#> https://github.com/leekgroup/recount - R package version 1.27.0,
#> <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 = {2023},
#> url = {http://www.bioconductor.org/packages/recount},
#> note = {https://github.com/leekgroup/recount - R package version 1.27.0},
#> 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
#> <https://doi.org/10.1186/1471-2105-12-449>,
#> <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 <https://doi.org/10.1101/618025>,
#> <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
#> <https://doi.org/10.1101/gr.254656.119>,
#> <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.
For more details, check the dev directory.
This package was developed using biocthis.
Teams involved
- Jeff Leek’s lab at JHBSPH Biostatistics Department,
- Ben Langmead’s lab at JHU Computer Science,
- Kasper Daniel Hansen’s lab at JHBSPH Biostatistics Department,
- Leonardo Collado-Torres and Andrew E. Jaffe from LIBD,
- Abhinav Nellore’s lab at OHSU,
- Data hosted by SciServer at JHU.
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