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: 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, Victor Pena

Maintainer: David Rossell <rosselldavid at gmail.com>

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 DesignRNASeq.pdf
PDF R Script Manual for the casper library
PDF   Reference Manual

Details

biocViews DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software, Transcription
Version 2.0.2
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, GenomeInfoDb, GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer, S4Vectors, sqldf, survival, VGAM
LinkingTo
Suggests
SystemRequirements
Enhances parallel
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source casper_2.0.2.tar.gz
Windows Binary casper_2.0.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) casper_2.0.2.tgz
Mac OS X 10.9 (Mavericks) casper_2.0.2.tgz
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