To cite package ‘scPipe’ in publications use:

  Tian, L., Su, S., Dong, X., Amann-Zalcenstein, D., Biben, C., Seidi,
  A., ... & Ritchie, M. E. (2018). scPipe: A flexible R/Bioconductor
  preprocessing pipeline for single-cell RNA-sequencing data. PLoS
  computational biology, 14(8), e1006361.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data},
    author = {{Tian} and {Luyi} and {Su} and {Shian} and {Dong} and {Xueyi} and {Amann-Zalcenstein} and {Daniela} and {Biben} and {Christine} and {Seidi} and {Azadeh} and {Hilton} and Douglas J and {Naik} and Shalin H and {Ritchie} and Matthew E},
    journal = {PLoS computational biology},
    volume = {14},
    number = {8},
    pages = {e1006361},
    year = {2018},
    publisher = {Public Library of Science},
  }

  Amarasinghe, S. L., Yang, P., Voogd, O., Yang, H., Du, M., Su, S.,
  ... & Ritchie, M. E. (2023). scPipe: An extended preprocessing
  pipeline for comprehensive single-cell ATAC-Seq data integration in
  R/Bioconductor. bioRxiv, 2023-09.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Shanika L. Amarasinghe and Phil Yang and Oliver Voogd and Haoyu Yang and Mei R. M. Du and Shian Su and Daniel V. Brown and Jafar S. Jabbari and Rory Bowden and Matthew E. Ritchie},
    title = {scPipe: An extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor},
    year = {2023},
    doi = {10.1101/2023.09.25.559230},
    publisher = {Cold Spring Harbor Laboratory},
    url = {https://www.biorxiv.org/content/early/2023/09/25/2023.09.25.559230},
    journal = {bioRxiv},
  }