Package: casper
Version: 1.4.0
Date: 2013-10-11
Title: Characterization of Alternative Splicing based on Paired-End
        Reads
Author: David Rossell, Camille Stephan-Otto, Manuel Kroiss, Miranda Stobbe
Maintainer: David Rossell <rosselldavid@gmail.org>
Depends: R (>= 2.14.1), Biobase, IRanges, methods, gtools,
        GenomicRanges, Rsamtools, plyr, gaga
Imports: VGAM, mgcv, GenomicFeatures, survival, sqldf
Enhances: parallel
Description: 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. 
License: GPL (>=2)
LazyLoad: yes
Collate: GenericDefs.R ClassDefinitions.R calcDenovo.R calcExp.R
        createDenovoGenome.R genePlot.R getDistrs.R getRoc.R
        denovoExpr.R mergeBatches.R mergeExp.R modelPrior.R
        pathCounts.R probNonEquiv.R procBam.R procGenome.R
        rmShortInserts.R simMultSamples.R simPost.R simReads.R
        splitGenomeByLength.R truncnorm.R wrapKnown.R
biocViews: Bioinformatics, GeneExpression, DifferentialExpression,
        Transcription, RNASeq, HighThroughputSequencing
Packaged: 2013-10-15 08:13:20 UTC; biocbuild
Built: R 3.0.2; i386-w64-mingw32; 2013-10-15 14:53:23 UTC; windows
Archs: i386, x64
