| annotatePTC | PTC and NMD-sensitivity detection from assembled RNA-seq data |
| CDSSet | Container for coding sequence (CDS) annotation information |
| CDSSet-class | Container for coding sequence (CDS) annotation information |
| conditions | Returns sample condictions of an SpliceRList or an CuffSet object |
| dim.SpliceRList | Retrieve the Dimensions of a SpliceRList |
| exons | Returns the transcript or exon GRanges from a SpliceRList object |
| generateGTF | Generate GTF files for transcript visualization in genome browsers |
| getCDS | Retrieve CDS information from UCSC |
| length.SpliceRList | Retrieve the Dimensions of a SpliceRList |
| prepareCuff | Prepare assembled RNA-seq data from Cufflinks for spliceR |
| prepareCuffExample | Prepare the Cufflinks example data |
| preSpliceRFilter | Filters on spliceR-lists for reduction of data sets |
| spliceR | Splice class detection from assembled RNA-seq data |
| SpliceRList | Transcript data and annotation object for spliceR |
| SpliceRList-class | Transcript data and annotation object for spliceR |
| 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 |