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

A BibTeX entry for LaTeX users is

  @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},
  }

  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).

A BibTeX entry for LaTeX users is

  @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},
  }

  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).

A BibTeX entry for LaTeX users is

  @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},
  }

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.