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 |