To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("casper")
In most cases, you don't need to download the package archive at all.
casper
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Characterization of Alternative Splicing based on Paired-End Reads
Bioconductor version: Release (3.1)
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 and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("casper")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("casper")
| DesignRNASeq.pdf | ||
| R Script | Manual for the casper library | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software, Transcription |
| Version | 2.2.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (2.5 years) |
| License | GPL (>=2) |
| Depends | R (>= 2.14.1), Biobase, IRanges, methods, GenomicRanges |
| Imports | BiocGenerics, EBarrays, gaga, gtools, GenomeInfoDb, GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer, S4Vectors, sqldf, survival, VGAM |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | parallel |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | casper_2.2.0.tar.gz |
| Windows Binary | casper_2.2.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | casper_2.2.0.tgz |
| Mac OS X 10.9 (Mavericks) | casper_2.2.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/casper/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/casper/ |
| Package Downloads Report | Download Stats |
Documentation »
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