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 (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


To view documentation for the version of this package installed in your system, start R and enter:



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


biocViews DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription
Version 2.37.0
In Bioconductor since BioC 2.12 (R-3.0) (10.5 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
Enhances parallel
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package casper_2.37.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: