To cite the decontX package, please cite the method you used.

If you used decontX() for single-cell RNA-seq data, cite:

Yang S, Corbett S, Koga Y, Wang Z, Johnson W, Yajima M, Campbell J (2020). “Decontamination of ambient RNA in single-cell RNA-seq with DecontX.” Genome Biology, 21(1), 57. doi:10.1186/s13059-020-1950-6.

If you used decontPro() for single-cell protein expression data, cite:

Yin Y, Yajima M, Campbell J (2024). “Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro.” Nucleic Acids Research, 52(1), e4. doi:10.1093/nar/gkad1032.

Corresponding BibTeX entries:

  @Article{,
    title = {Decontamination of ambient RNA in single-cell RNA-seq with
      DecontX},
    author = {Shiyi Yang and Sean E. Corbett and Yusuke Koga and Zhe
      Wang and W. Evan Johnson and Masanao Yajima and Joshua D.
      Campbell},
    journal = {Genome Biology},
    year = {2020},
    volume = {21},
    number = {1},
    pages = {57},
    doi = {10.1186/s13059-020-1950-6},
  }

  @Article{,
    title = {Characterization and decontamination of background noise
      in droplet-based single-cell protein expression data with
      DecontPro},
    author = {Yuan Yin and Masanao Yajima and Joshua D. Campbell},
    journal = {Nucleic Acids Research},
    year = {2024},
    volume = {52},
    number = {1},
    pages = {e4},
    doi = {10.1093/nar/gkad1032},
  }