Package: casper
Version: 2.2.0
Date: 2015-01-29
Title: Characterization of Alternative Splicing based on Paired-End
        Reads
Author: David Rossell, Camille Stephan-Otto, Manuel Kroiss, Miranda
        Stobbe, Victor Pena
Maintainer: David Rossell <rosselldavid@gmail.com>
Depends: R (>= 2.14.1), Biobase, IRanges, methods, GenomicRanges
Imports: BiocGenerics, EBarrays, gaga, gtools, GenomeInfoDb,
        GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer,
        S4Vectors, 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 asymmetryCheck.R calcDenovo.R
        calcExp.R casperVignettes.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 qqnormGenomeWide.R
        relexprByGene.R rmShortInserts.R simMultSamples.R simPost.R
        simReads.R splitGenomeByLength.R truncnorm.R wrapKnown.R
        checks.R wrapDenovo.R
biocViews: GeneExpression, DifferentialExpression, Transcription,
        RNASeq, Sequencing
NeedsCompilation: yes
Packaged: 2015-04-17 04:20:05 UTC; biocbuild
Built: R 3.2.0; i386-w64-mingw32; 2015-04-17 07:04:36 UTC; windows
Archs: i386, x64
