To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("casper")

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

casper

DOI: 10.18129/B9.bioc.casper    

Characterization of Alternative Splicing based on Paired-End Reads

Bioconductor version: Release (3.6)

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:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/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 2.12.0
In Bioconductor since BioC 2.12 (R-3.0) (4.5 years)
License GPL (>=2)
Depends R (>= 2.14.1), Biobase, IRanges, methods, GenomicRanges
Imports BiocGenerics, coda, EBarrays, gaga, gtools, GenomeInfoDb, GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer, S4Vectors(>= 0.9.25), 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.

Source Package casper_2.12.0.tar.gz
Windows Binary casper_2.12.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) casper_2.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/casper
Package Short Url http://bioconductor.org/packages/casper/
Package Downloads Report Download Stats

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