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