refs.bib

@ARTICLE{Amarasinghe2020-longread,
  title    = "Opportunities and challenges in long-read sequencing data
              analysis",
  author   = "Amarasinghe, Shanika L and Su, Shian and Dong, Xueyi and Zappia,
              Luke and Ritchie, Matthew E and Gouil, Quentin",
  journal  = "Genome Biology",
  volume   =  21,
  number   =  1,
  pages    = "30",
  year     =  2020
}

@ARTICLE{Raghavan2022-denovo,
  title    = "A simple guide to de novo transcriptome assembly and annotation",
  author   = "Raghavan, Venket and Kraft, Louis and Mesny, Fantin and Rigerte,
              Linda",
  journal  = "Briefings in Bioinformatics",
  volume   =  23,
  number   =  2,
  year     =  2022
}


@ARTICLE{Zhu2019-swish,
  title    = "Nonparametric expression analysis using inferential replicate
              counts",
  author   = "Zhu, Anqi and Srivastava, Avi and Ibrahim, Joseph G and Patro,
              Rob and Love, Michael I",
  journal  = "Nucleic Acids Research",
  volume   =  47,
  number   =  18,
  pages    = "e105",
  year     =  2019,
}

@UNPUBLISHED{Baldoni2023-catchsalmon,
  title    = "Dividing out quantification uncertainty allows efficient
              assessment of differential transcript expression",
  author   = "Baldoni, Pedro L and Chen, Yunshun and Hediyeh-zadeh, Soroor and
              Liao, Yang and Dong, Xueyi and Ritchie, Matthew E and Shi, Wei
              and Smyth, Gordon K",
  journal  = "bioRxiv",
  pages    = "2023.04.02.535231",
  year     =  2023,
}

@ARTICLE{Love2018-swimming,
  title    = "Swimming downstream: statistical analysis of differential
              transcript usage following Salmon quantification",
  author   = "Love, Michael I and Soneson, Charlotte and Patro, Rob",
  journal  = "F1000Res.",
  volume   =  7,
  year     =  2018
}