To cite the comparative chi-squared test in publications, use

Song M, Zhang Y, Katzaroff AJ, Edgar BA, Buttitta L (2014). “Hunting complex differential gene interaction patterns across molecular contexts.” Nucleic Acids Research, 42(7), e57. doi:10.1093/nar/gku086.

Zhang Y, Liu ZL, Song M (2015). “ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion.” Nucleic Acids Research, 43(9), 4393–4407. doi:10.1093/nar/gkv358.

To cite the entire package in publications, use

Sharma R, Song J (2021). DiffXTables: Pattern Analysis Across Contingency Tables. Comprehensive R Archive Network. R package, https://CRAN.R-project.org/package=DiffXTables.

To cite the marginal-change test, the strength test, and type analysis on multiple contingency tables in publications, use

Sharma R, Luo X, Kumar S, Song M (2020). “Three co-expression pattern types across microbial transcriptional networks of plankton in two oceanic waters.” In Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB '20), series BCB '20. ISBN 9781450379649, doi:10.1145/3388440.3412485, https://doi.org/10.1145/3388440.3412485.

To cite the Sharma-Song test in publications, use

Sharma R, Kumar S, Song M (2021). “Fundamental gene network rewiring at the second order within and across mammalian systems.” Bioinformatics. doi:10.1093/bioinformatics/btab240.

Corresponding BibTeX entries:

  @Article{song2014hunting,
    title = {Hunting complex differential gene interaction patterns
      across molecular contexts},
    journal = {Nucleic Acids Research},
    year = {2014},
    volume = {42},
    number = {7},
    pages = {e57},
    author = {Mingzhou Song and Yang Zhang and Alexia J. Katzaroff and
      Bruce A. Edgar and Laura Buttitta},
    doi = {10.1093/nar/gku086},
  }

  @Article{zhang2015chinet,
    title = {{ChiNet} uncovers rewired transcription subnetworks in
      tolerant yeast for advanced biofuels conversion},
    journal = {Nucleic Acids Research},
    year = {2015},
    volume = {43},
    number = {9},
    pages = {4393--4407},
    author = {Yang Zhang and Z. Lewis Liu and Mingzhou Song},
    doi = {10.1093/nar/gkv358},
  }

  @Manual{sharma2021diffxtables,
    title = {DiffXTables: Pattern Analysis Across Contingency Tables},
    author = {Ruby Sharma and Joe Song},
    year = {2021},
    note = {Comprehensive R Archive Network. R package},
    url = {https://CRAN.R-project.org/package=DiffXTables},
  }

  @InProceedings{sharma2020COPTYP,
    author = {Ruby Sharma and Xuye Luo and Sajal Kumar and Mingzhou
      Song},
    booktitle = {Proceedings of the 11th ACM International Conference
      on Bioinformatics, Computational Biology, and Health Informatics
      {(BCB '20)}},
    title = {Three co-expression pattern types across microbial
      transcriptional networks of plankton in two oceanic waters},
    year = {2020},
    isbn = {9781450379649},
    articleno = {14},
    numpages = {10},
    publisher = {Association for Computing Machinery},
    address = {New York, NY, USA},
    url = {https://doi.org/10.1145/3388440.3412485},
    doi = {10.1145/3388440.3412485},
    keywords = {Planktonic microbial community, Metatranscriptome,
      Oceanic ecosystem, Co-expression network, First-order
      differential pattern},
    location = {Virtual Event, USA},
    series = {BCB '20},
  }

  @Article{,
    key = {ruby2021/BIOINF-2020-0795},
    author = {Ruby Sharma and Sajal Kumar and Mingzhou Song},
    title = {Fundamental gene network rewiring at the second order
      within and across mammalian systems},
    year = {2021},
    journal = {Bioinformatics},
    doi = {10.1093/bioinformatics/btab240},
  }