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. 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://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.

Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT (2026). Explore and download data from the recount project. doi:10.18129/B9.bioc.recount. https://github.com/leekgroup/recount - R package version 1.39.0, http://www.bioconductor.org/packages/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.

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.

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.

Corresponding BibTeX entries:

  @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},
  }

  @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},
  }

  @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},
  }

  @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 = {2026},
    url = {http://www.bioconductor.org/packages/recount},
    note = {https://github.com/leekgroup/recount - R package version
      1.39.0},
    doi = {10.18129/B9.bioc.recount},
  }

  @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},
  }

  @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},
  }

  @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},
  }