Package: casper
Version: 1.9.0
Date: 2014-05-29
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, GenomicRanges
Imports: BiocGenerics, EBarrays, gaga, gtools, GenomicFeatures, mgcv,
        Rsamtools, rtracklayer, sqldf, survival, VGAM
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 makeTranscriptDbFromGFF.R mergeBatches.R
        mergeExp.R modelPrior.R pathCounts.R probNonEquiv.R procBam.R
        procGenome.R relexprByGene.R rmShortInserts.R simMultSamples.R
        simPost.R simReads.R splitGenomeByLength.R truncnorm.R
        wrapKnown.R
biocViews: GeneExpression, DifferentialExpression, Transcription,
        RNASeq, Sequencing
Packaged: 2014-05-31 06:14:56 UTC; biocbuild
Built: R 3.1.0; x86_64-apple-darwin10.8.0; 2014-05-31 11:25:30 UTC; unix
