To cite the scp package in publications use:

Vanderaa, Christophe, and Laurent Gatto. 2023. Revisiting the Thorny Issue of Missing Values in Single-Cell Proteomics. Journal of Proteome Research 22 (9): 2775–84.

Vanderaa Christophe and Laurent Gatto. The current state of single-cell proteomics data analysis. Current Protocols 3 (1): e658.; doi: https://doi.org/10.1002/cpz1.658 (2023).

Vanderaa Christophe and Laurent Gatto. Replication of Single-Cell Proteomics Data Reveals Important Computational Challenges. Expert Review of Proteomics, 1–9 (2021).

Vanderaa Christophe and Laurent Gatto. scplainer: using linear models to understand mass spectrometry-based single-cell proteomics data. Genome Biol 26, 237 (2025). https://doi.org/10.1186/s13059-025-03713-4

Corresponding BibTeX entries:

  @Article{,
    title = {Revisiting the thorny issue of missing values in
      single-cell proteomics},
    author = {Christophe Vanderaa and Laurent Gatto},
    journal = {J. Proteome Res.},
    volume = {22},
    number = {9},
    pages = {2775--2784},
    month = {sep},
    year = {2023},
  }

  @Article{,
    title = {The current state of single-cell proteomics data
      analysis},
    author = {Christophe Vanderaa and Laurent Gatto},
    journal = {Current Protocols},
    year = {2023},
    pages = {e658},
  }

  @Article{,
    title = {Replication of Single-Cell Proteomics Data Reveals
      Important Computational Challenges},
    author = {Christophe Vanderaa and Laurent Gatto},
    journal = {Expert Review of Proteomics},
    year = {2021},
    pages = {1-9},
  }

  @Article{,
    title = {scplainer: using linear models to understand mass
      spectrometry-based single-cell proteomics data},
    author = {Christophe Vanderaa and Laurent Gatto},
    journal = {Genome Biol},
    year = {2025},
    volume = {26},
    doi = {10.1186/s13059-025-03713-4},
  }