Authors and Citation

Authors

• Daiki Kumakura. Author, maintainer.

Citation

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

@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.

@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.

@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.

@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},
}

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@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.

@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.

@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.

@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},
}