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 (3.20)
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("casper")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("casper")
DesignRNASeq.pdf | ||
Manual for the casper library | R Script | |
Reference Manual |
Details
biocViews | DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription |
Version | 2.39.0 |
In Bioconductor since | BioC 2.12 (R-3.0) (11.5 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 |
System Requirements | |
URL |
See More
Suggests | |
Linking To | |
Enhances | parallel |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | casper_2.39.0.tar.gz |
Windows Binary | casper_2.39.0.zip |
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 |