casper

DOI: 10.18129/B9.bioc.casper    

This is the development version of casper; for the stable release version, see casper.

Characterization of Alternative Splicing based on Paired-End Reads

Bioconductor version: Development (3.13)

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, Victor Pena

Maintainer: David Rossell <rosselldavid at gmail.com>

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

Installation

To install this package, start R (version "4.1") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("casper")

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

Documentation

PDF   Reference Manual

Details

biocViews DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription
Version 2.25.1
In Bioconductor since BioC 2.12 (R-3.0) (7.5 years)
License GPL (>=2)
Depends R (>= 3.6.0), Biobase, IRanges, methods, GenomicRanges
Imports BiocGenerics(>= 0.31.6), coda, EBarrays, gaga, gtools, GenomeInfoDb, GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer, S4Vectors(>= 0.9.25), sqldf, survival, VGAM
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Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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/
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