casper

Characterization of Alternative Splicing based on Paired-End Reads

Bioconductor version: Development (3.0)

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, Miranda Stobbe

Maintainer: David Rossell <rosselldavid at gmail.org>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("casper")

To cite this package in a publication, start R and enter:

    citation("casper")

Documentation

PDF R Script Manual for the casper library
PDF   Reference Manual

Details

biocViews DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software, Transcription
Version 1.7.0
In Bioconductor since BioC 2.12 (R-3.0)
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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Package Downloads

Package Source casper_1.7.0.tar.gz
Windows Binary casper_1.7.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) casper_1.7.0.tgz
Mac OS X 10.9 (Mavericks)
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