Classification of alternative splicing and prediction of coding potential from RNA-seq data.


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Documentation for package ‘spliceR’ version 1.6.2

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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