Please use the first reference below to cite the eisaR software itself, the second reference (Gaidatzis et al.) to cite the EISA paper, or the third (Soneson et al.) to cite the preprocessing analysis for RNA velocity.

Stadler MB, Gaidatzis D, Burger L and Soneson C. eisaR: Exon-Intron Split Analysis (EISA) in R. R package version 1.0

Gaidatzis D, Burger L, Florescu M and Stadler MB. Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation. Nature Biotechnology 33(7):722-729 (2015).

Soneson C, Srivastava A, Patro R and Stadler MB. Preprocessing choices affect RNA velocity results for droplet scRNA-seq data. PLoS Computational Biology 17(1):e1008585 (2021).

This free open-source software implements academic research by the authors and co-workers. If you use it, please support the project by citing the appropriate journal articles.

Corresponding BibTeX entries:

  @Manual{,
    title = {eisaR: Exon-Intron Split Anaalysis (EISA) in R},
    author = {Michael B Stadler and Dimos Gaidatzis and Lukas Burger
      and Charlotte Soneson},
    year = {2020},
    note = {R package version 1.0},
  }

  @Article{,
    title = {Analysis of intronic and exonic reads in RNA-seq data
      characterizes transcriptional and post-transcriptional
      regulation},
    author = {Dimos Gaidatzis and Lukas Burger and Michael B Stadler},
    journal = {Nature Biotechnology},
    volume = {33},
    number = {7},
    pages = {722--729},
    year = {2015},
    note = {PMID:26098447},
    doi = {10.1038/nbt.3269},
  }

  @Article{,
    title = {Preprocessing choices affect RNA velocity results for
      droplet scRNA-seq data},
    author = {Charlotte Soneson and Avi Srivastava and Rob Patro and
      Michael B Stadler},
    journal = {PLoS Computational Biology},
    volume = {17},
    number = {1},
    pages = {e1008585},
    year = {2021},
    note = {PMID:33428615},
    doi = {10.1371/journal.pcbi.1008585},
  }