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

casper

Characterization of Alternative Splicing based on Paired-End Reads

Bioconductor version: 2.13

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>

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("casper")

 

PDF	R Script	Manual for the casper library
PDF		Reference Manual

Details

biocViews	Bioinformatics, DifferentialExpression, GeneExpression, HighThroughputSequencing, RNASeq, Software, Transcription
Version	1.4.0
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 Archives

Follow Installation instructions to use this package in your R session.

Package Source	casper_1.4.0.tar.gz
Windows Binary	casper_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	casper_1.4.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats