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.

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.

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.

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.

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.

Korotkevich G, Sukhov V, Budin N, Shpak B, Artyomov M, Sergushichev A (2021). “Fast gene set enrichment analysis.” bioRxiv. 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.

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.

Corresponding BibTeX entries:

  @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},
  }

  @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},
  }

  @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},
  }

  @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},
  }

  @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},
  }

  @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},
  }

  @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},
  }

  @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},
  }