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.

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.

Corresponding BibTeX entries:

  @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},
  }

  @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},
  }