casper

DOI: 10.18129/B9.bioc.casper    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see casper.

Characterization of Alternative Splicing based on Paired-End Reads

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("casper")

For older versions of R, please refer to the appropriate Bioconductor release.

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, ImmunoOncology, RNASeq, Sequencing, Software, Transcription
Version	2.18.0
In Bioconductor since	BioC 2.12 (R-3.0) (6.5 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
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Enhances	parallel
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Build Report

Package Archives

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

Source Package	casper_2.18.0.tar.gz
Windows Binary	casper_2.18.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	casper_2.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/casper
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/casper
Package Short Url	https://bioconductor.org/packages/casper/
Package Downloads Report	Download Stats