Characterization of Alternative Splicing based on Paired-End Reads

Bioconductor version: Release (2.12)

Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.

Author: David Rossell, Camille Stephan-Otto, Manuel Kroiss

Maintainer: David Rossell <rosselldavid at>

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PDF R Script Manual for the casper library
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biocViews Bioinformatics, DifferentialExpression, GeneExpression, HighThroughputSequencing, RNASeq, Software, Transcription
Version 1.1.2
In Bioconductor since BioC 2.13 (R-2.18)
License GPL (>=2)
Depends R (>= 2.14.1), Biobase, IRanges, methods, gtools, GenomicRanges, Rsamtools, plyr, gaga
Imports VGAM, mgcv, GenomicFeatures, survival, sqldf
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Depends On Me
Imports Me
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