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spliceR (version 1.14.0)

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

Description

An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.

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Version

Version

1.14.0

License

GPL (>=2)

Maintainer

Johannes Waage

Last Published

February 15th, 2017

Functions in spliceR (1.14.0)

prepareCuffExample

Prepare the Cufflinks example data
totalNumberOfAS

Returns total number of alternative splicing events
annotatePTC

PTC and NMD-sensitivity detection from assembled RNA-seq data
SpliceRList

Transcript data and annotation object for spliceR
generateGTF

Generate GTF files for transcript visualization in genome browsers
spliceRPlot

Plot venn diagrams of alternative splicing events
conditions

Returns sample condictions of an SpliceRList or an CuffSet object
topIsoShift

Returns top transcripts in terms of isoform switching
getCDS

Retrieve CDS information from UCSC
dim

Retrieve the Dimensions of a SpliceRList
spliceR

Splice class detection from assembled RNA-seq data
prepareCuff

Prepare assembled RNA-seq data from Cufflinks for spliceR
CDSSet

Container for coding sequence (CDS) annotation information
transcripts

Returns the transcript or exon GRanges from a SpliceRList object
preSpliceRFilter

Filters on spliceR-lists for reduction of data sets