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casper

Characterization of Alternative Splicing based on Paired-End Reads


Bioconductor version: Release (3.18)

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 "4.3") and enter:


if (!require("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")
DesignRNASeq.pdf PDF
Manual for the casper library PDF R Script
Reference Manual PDF

Details

biocViews DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription
Version 2.36.0
In Bioconductor since BioC 2.12 (R-3.0) (11 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 casper_2.36.0.tar.gz
Windows Binary casper_2.36.0.zip (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/casper
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/casper
Bioc Package Browser https://code.bioconductor.org/browse/casper/
Package Short Url https://bioconductor.org/packages/casper/
Package Downloads Report Download Stats