@article{Katz22012015,
  author = {Katz, Yarden and Wang, Eric T. and Silterra, Jacob and Schwartz, Schraga and Wong, Bang and Thorvaldsdóttir, Helga and Robinson, James T. and Mesirov, Jill P. and Airoldi, Edoardo M. and Burge, Christopher B.},
  title = {Quantitative visualization of alternative exon expression from RNA-seq data},
  year = {2015},
  doi = {10.1093/bioinformatics/btv034},
  abstract ={Motivation: Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority of human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing and other mechanisms, and that most alternative isoforms vary in expression between human tissues. As RNA-Seq datasets grow in size, it remains challenging to visualize isoform expression across multiple samples.Results: To help address this problem, we present Sashimi plots, a quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. Sashimi plots can be made using the Broad Integrated Genome Viewer or with a stand-alone command line program.Availability and implementation: Software code and documentation freely available here: http://miso.readthedocs.org/en/fastmiso/sashimi.htmlContact: mesirov@broadinstitute.org, airoldi@fas.harvard.edu or cburge@mit.eduSupplementary information: Supplementary data are available at Bioinformatics online.},
  URL = {http://bioinformatics.oxfordjournals.org/content/early/2015/02/25/bioinformatics.btv034.abstract},
  eprint = {http://bioinformatics.oxfordjournals.org/content/early/2015/02/25/bioinformatics.btv034.full.pdf+html},
  journal = {Bioinformatics}
}

@InBook{Hahne2016,
  author = {Florian Hahne and Robert Ivanek},
  editor = {Ewy Math{\'e} and Sean Davis},
  chapter = {Visualizing Genomic Data Using Gviz and Bioconductor},
  title = {Statistical Genomics: Methods and Protocols},
  year = {2016},
  publisher = {Springer New York},
  address = {New York, NY},
  pages = {335--351},
  isbn = {978-1-4939-3578-9},
  doi = {10.1007/978-1-4939-3578-9_16},
  url = {http://dx.doi.org/10.1007/978-1-4939-3578-9_16},
}
