Cite scp workflow chapter

[lgatto]

Cite the new scp workflow in the vignette.

[cvanderaa]

The SCP citation is currently:

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).

We could/should also add the scplainer (bioRxiv) paper, and Sam's paper. But I feel that adding more references will confuse the users that want to cite the software. What do you think?

[lgatto]

• It's important to add them. The individual references can be specified in the respective vignettes.
• Is it possible to specify sections or explanations of what is what in the citation file?

[cvanderaa]

Yes it's possible to add descriptions as citation headers. Here is a tentative state for the citation, I'm of course open to change:

citation("scp")

To cite the scp package in publications, please use at least one of the
relevant citations below.

1. Software for SCP data processing:

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

2. Modelling of SCP data:

  Vanderaa Christophe and Laurent Gatto. scplainer: using linear models
  to understand mass spectrometry-based single-cell proteomics data.
  bioRxiv 2023.12.14.571792; doi:
  https://doi.org/10.1101/2023.12.14.571792

3. Management and reporting of missing values in SCP data:

  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.

4. Reproduction of SCP data processing workflows:

  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).

5. Standardised workflow for SCP data processing:

  Grégoire, S. et al. Mass Spectrometry Based Single Cell Proteomics.
  (Springer US, 2023).

To see these entries in BibTeX format, use 'print(<citation>,
bibtex=TRUE)', 'toBibtex(.)', or set
'options(citation.bibtex.max=999)'.