casper
Characterization of Alternative Splicing based on Paired-End Reads
Bioconductor version: Release (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 gmail.com>
citation("casper")):
Installation
To install this package, start R (version "4.4") 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 | ||
| Manual for the casper library | R Script | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription |
| Version | 2.38.0 |
| 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_2.38.0.tar.gz |
| Windows Binary (x86_64) | casper_2.38.0.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 |