rsemflow coordinates established R/Bioconductor methods. Please cite
the methods used in your analysis:

  Kumakura D (2026). _rsemflow: Metadata-Driven Downstream Analysis for
  RSEM Gene-Level Results_. R package version 0.1.1,
  <https://github.com/DaikiKumakura/rsemflow>.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {rsemflow: Metadata-Driven Downstream Analysis for RSEM Gene-Level Results},
    author = {Daiki Kumakura},
    year = {2026},
    note = {R package version 0.1.1},
    url = {https://github.com/DaikiKumakura/rsemflow},
  }

  Li B, Dewey C (2011). “RSEM: accurate transcript quantification from
  RNA-Seq data with or without a reference genome.” _BMC
  Bioinformatics_, *12*, 323. doi:10.1186/1471-2105-12-323
  <https://doi.org/10.1186/1471-2105-12-323>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome},
    author = {Bo Li and Colin N. Dewey},
    journal = {BMC Bioinformatics},
    year = {2011},
    volume = {12},
    pages = {323},
    doi = {10.1186/1471-2105-12-323},
  }

  Soneson C, Love M, Robinson M (2015). “Differential analyses for
  RNA-seq: transcript-level estimates improve gene-level inferences.”
  _F1000Research_, *4*, 1521. doi:10.12688/f1000research.7563.2
  <https://doi.org/10.12688/f1000research.7563.2>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences},
    author = {Charlotte Soneson and Michael I. Love and Mark D. Robinson},
    journal = {F1000Research},
    year = {2015},
    volume = {4},
    pages = {1521},
    doi = {10.12688/f1000research.7563.2},
  }

  Love M, Huber W, Anders S (2014). “Moderated estimation of fold
  change and dispersion for RNA-seq data with DESeq2.” _Genome
  Biology_, *15*, 550. doi:10.1186/s13059-014-0550-8
  <https://doi.org/10.1186/s13059-014-0550-8>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
    author = {Michael I. Love and Wolfgang Huber and Simon Anders},
    journal = {Genome Biology},
    year = {2014},
    volume = {15},
    pages = {550},
    doi = {10.1186/s13059-014-0550-8},
  }

  Subramanian A, Tamayo P, Mootha V, Mukherjee S, Ebert B, Gillette M,
  Paulovich A, Pomeroy S, Golub T, Lander E, Mesirov J (2005). “Gene
  set enrichment analysis: a knowledge-based approach for interpreting
  genome-wide expression profiles.” _Proceedings of the National
  Academy of Sciences_, *102*(43), 15545-15550.
  doi:10.1073/pnas.0506580102
  <https://doi.org/10.1073/pnas.0506580102>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles},
    author = {Aravind Subramanian and Pablo Tamayo and Vamsi K. Mootha and Sayan Mukherjee and Benjamin L. Ebert and Michael A. Gillette and Amanda Paulovich and Scott L. Pomeroy and Todd R. Golub and Eric S. Lander and Jill P. Mesirov},
    journal = {Proceedings of the National Academy of Sciences},
    year = {2005},
    volume = {102},
    number = {43},
    pages = {15545--15550},
    doi = {10.1073/pnas.0506580102},
  }

  Korotkevich G, Sukhov V, Budin N, Shpak B, Artyomov M, Sergushichev A
  (2021). “Fast gene set enrichment analysis.” _bioRxiv_.
  doi:10.1101/060012 <https://doi.org/10.1101/060012>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Fast gene set enrichment analysis},
    author = {Gennady Korotkevich and Vladimir Sukhov and Nikolay Budin and Boris Shpak and Maxim N. Artyomov and Alexey Sergushichev},
    journal = {bioRxiv},
    year = {2021},
    doi = {10.1101/060012},
  }

  Hänzelmann S, Castelo R, Guinney J (2013). “GSVA: gene set variation
  analysis for microarray and RNA-seq data.” _BMC Bioinformatics_,
  *14*, 7. doi:10.1186/1471-2105-14-7
  <https://doi.org/10.1186/1471-2105-14-7>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {GSVA: gene set variation analysis for microarray and RNA-seq data},
    author = {Sonja Hänzelmann and Robert Castelo and Justin Guinney},
    journal = {BMC Bioinformatics},
    year = {2013},
    volume = {14},
    pages = {7},
    doi = {10.1186/1471-2105-14-7},
  }

  Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov J, Tamayo
  P (2015). “The Molecular Signatures Database Hallmark Gene Set
  Collection.” _Cell Systems_, *1*(6), 417-425.
  doi:10.1016/j.cels.2015.12.004
  <https://doi.org/10.1016/j.cels.2015.12.004>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {The Molecular Signatures Database Hallmark Gene Set Collection},
    author = {Arthur Liberzon and Chet Birger and Helga Thorvaldsdóttir and Mahmoud Ghandi and Jill P. Mesirov and Pablo Tamayo},
    journal = {Cell Systems},
    year = {2015},
    volume = {1},
    number = {6},
    pages = {417--425},
    doi = {10.1016/j.cels.2015.12.004},
  }