CDSSet                  Container for coding sequence (CDS) annotation
                        information
SpliceRList             Transcript data and annotation object for
                        spliceR
annotatePTC             PTC and NMD-sensitivity detection from
                        assembled RNA-seq data
conditions              Returns sample condictions of an SpliceRList or
                        an CuffSet object
dim.SpliceRList         Retrieve the Dimensions of a SpliceRList
generateGTF             Generate GTF files for transcript visualization
                        in genome browsers
getCDS                  Retrieve CDS information from UCSC
preSpliceRFilter        Filters on spliceR-lists for reduction of data
                        sets
prepareCuff             Prepare assembled RNA-seq data from Cufflinks
                        for spliceR
prepareCuffExample      Prepare the Cufflinks example data
spliceR                 Splice class detection from assembled RNA-seq
                        data
spliceRPlot             Plot venn diagrams of alternative splicing
                        events
topIsoShift             Returns top transcripts in terms of isoform
                        switching
totalNumberOfAS         Returns total number of alternative splicing
                        events
transcripts             Returns the transcript or exon GRanges from a
                        SpliceRList object
