casper
Characterization of Alternative Splicing based on Paired-End Reads
Bioconductor version: Release (2.12)
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
Maintainer: David Rossell <rosselldavid at gmail.org>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("casper")
To cite this package in a publication, start R and enter:
citation("casper")
Documentation
| R Script | Manual for the casper library | |
| Reference Manual |
Details
| biocViews | Bioinformatics, DifferentialExpression, GeneExpression, HighThroughputSequencing, RNASeq, Software, Transcription |
| Version | 1.1.2 |
| In Bioconductor since | BioC 2.13 (R-2.18) |
| License | GPL (>=2) |
| Depends | R (>= 2.14.1), Biobase, IRanges, methods, gtools, GenomicRanges, Rsamtools, plyr, gaga |
| Imports | VGAM, mgcv, GenomicFeatures, survival, sqldf |
| Suggests | |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Downloads
| Package Source | casper_1.1.2.tar.gz |
| Windows Binary | casper_1.1.2.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | casper_1.1.2.tgz |
| Package Downloads Report | Download Stats |
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