To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

casper

Characterization of Alternative Splicing based on Paired-End Reads

Bioconductor version: Release (2.14)

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>

Citation (from within R, enter citation("casper")):

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 DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software, Transcription
Version 1.9.0
In Bioconductor since BioC 2.12 (R-3.0)
License GPL (>=2)
Depends R (>= 2.14.1), Biobase, IRanges, methods, GenomicRanges
Imports BiocGenerics, EBarrays, gaga, gtools, GenomicFeatures, mgcv, Rsamtools, rtracklayer, sqldf, survival, VGAM
Suggests
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Depends On Me
Imports Me
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Package Archives

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

Package Source casper_1.9.0.tar.gz
Windows Binary casper_1.9.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) casper_1.9.0.tgz
Mac OS X 10.9 (Mavericks) casper_1.9.0.tgz
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