title: spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.
abstract: BACKGROUND
  RNA-seq data is currently underutilized, in part because it is difficult to predict the functional impact of alternate transcription events. Recent software improvements in full-length transcript deconvolution prompted us to develop spliceR, an R package for classification of alternative splicing and prediction of coding potential.
  
  
  RESULTS
  spliceR uses the full-length transcript output from RNA-seq assemblers to detect single or multiple exon skipping, alternative donor and acceptor sites, intron retention, alternative first or last exon usage, and mutually exclusive exon events. For each of these events spliceR also annotates the genomic coordinates of the differentially spliced elements, facilitating downstream sequence analysis. For each transcript isoform fraction values are calculated to identify transcript switching between conditions. Lastly, spliceR predicts the coding potential, as well as the potential nonsense mediated decay (NMD) sensitivity of each transcript.
  
  
  CONCLUSIONS
  spliceR is an easy-to-use tool that extends the usability of RNA-seq and assembly technologies by allowing greater depth of annotation of RNA-seq data. spliceR is implemented as an R package and is freely available from the Bioconductor repository ( http://www.bioconductor.org/packages/2.13/bioc/html/spliceR.html).
authors.forename: Kristoffer
authors.initials: K
authors.lastname: Vitting-Seerup
authors.forename: Bo Torben
authors.initials: BT
authors.lastname: Porse
authors.affiliation: Department of Biology, The Bioinformatics Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK2200, Denmark. albin@binf.ku.dk.
authors.forename: Albin
authors.initials: A
authors.lastname: Sandelin
authors.forename: Johannes
authors.initials: J
authors.lastname: Waage
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D001483:Base Sequence; D005091:Exons / Q000235:genetics; D045325:HCT116 Cells; D006801:Humans; D007438:Introns / Q000235:genetics; D020033:Protein Isoforms / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D020033:Protein Isoforms; D012333:RNA, Messenger