Chen Y, Chen L, Lun ATL, Baldoni P, Smyth GK (2025). “edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets.” Nucleic Acids Research, 53(2), gkaf018. doi:10.1093/nar/gkaf018.

Dunn PK, Smyth GK (1996). “Randomized quantile residuals.” J. Comput. Graph. Statist, 5, 236-244.

Giner G, Smyth GK (2016). “statmod: probability calculations for the inverse Gaussian distribution.” R Journal, 8(1), 339-351.

Hu Y, Smyth GK (2009). “ELDA: extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays.” Journal of Immunological Methods, 347(1), 70-78.

Phipson B, Smyth GK (2010). “Permutation p-values should never be zero: calculating exact p-values when permutations are randomly drawn.” Statistical Applications in Genetics and Molecular Biology, 9(1), Article 39.

Smyth GK (2005). “Numerical integration.” Encyclopedia of Biostatistics, 3088-3095.

Smyth GK (2005). “Optimization and nonlinear equations.” Encyclopedia of Biostatistics, 3088-3095.

Smyth GK (2002). “An efficient algorithm for REML in heteroscedastic regression.” Journal of Computational and Graphical Statistics, 11, 836-847.

Corresponding BibTeX entries:

  @Article{,
    author = {Yunshun Chen and Lizhong Chen and Aaron T L Lun and Pedro
      Baldoni and Gordon K Smyth},
    title = {{edgeR} v4: powerful differential analysis of sequencing
      data with expanded functionality and improved support for small
      counts and larger datasets},
    year = {2025},
    journal = {Nucleic Acids Research},
    volume = {53},
    number = {2},
    pages = {gkaf018},
    doi = {10.1093/nar/gkaf018},
  }

  @Article{,
    author = {Peter K Dunn and Gordon K Smyth},
    year = {1996},
    title = {Randomized quantile residuals},
    journal = {J. Comput. Graph. Statist},
    volume = {5},
    pages = {236-244},
  }

  @Article{,
    author = {Goknur Giner and Gordon K Smyth},
    year = {2016},
    title = {statmod: probability calculations for the inverse Gaussian
      distribution},
    journal = {R Journal},
    volume = {8},
    number = {1},
    pages = {339-351},
  }

  @Article{,
    author = {Yifang Hu and Gordon K Smyth},
    year = {2009},
    title = {ELDA: extreme limiting dilution analysis for comparing
      depleted and enriched populations in stem cell and other assays},
    journal = {Journal of Immunological Methods},
    volume = {347},
    number = {1},
    pages = {70-78},
  }

  @Article{,
    author = {Belinda Phipson and Gordon K Smyth},
    year = {2010},
    title = {Permutation p-values should never be zero: calculating
      exact p-values when permutations are randomly drawn},
    journal = {Statistical Applications in Genetics and Molecular
      Biology},
    volume = {9},
    number = {1},
    pages = {Article 39},
  }

  @Article{,
    author = {Gordon K Smyth},
    title = {Numerical integration},
    journal = {Encyclopedia of Biostatistics},
    year = {2005},
    publisher = {John Wiley and Sons, Ltd},
    pages = {3088-3095},
  }

  @Article{,
    author = {Gordon K Smyth},
    title = {Optimization and nonlinear equations},
    journal = {Encyclopedia of Biostatistics},
    year = {2005},
    publisher = {John Wiley and Sons},
    pages = {3088-3095},
  }

  @Article{,
    author = {Gordon K Smyth},
    year = {2002},
    title = {An efficient algorithm for REML in heteroscedastic
      regression},
    journal = {Journal of Computational and Graphical Statistics},
    volume = {11},
    pages = {836-847},
  }