Package: casper
Version: 2.42.0
Date: 2024-03-18
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 (>= 3.6.0), Biobase, IRanges, methods, GenomicRanges
Imports: BiocGenerics (>= 0.31.6), coda, EBarrays, gaga, gtools,
        GenomeInfoDb, GenomicFeatures, limma, mgcv, Rsamtools,
        rtracklayer, S4Vectors (>= 0.9.25), 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: ImmunoOncology, GeneExpression, DifferentialExpression,
        Transcription, RNASeq, Sequencing
git_url: https://git.bioconductor.org/packages/casper
git_branch: RELEASE_3_21
git_last_commit: 8d20bff
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: yes
Packaged: 2025-04-15 23:31:30 UTC; biocbuild
Built: R 4.5.0; x86_64-w64-mingw32; 2025-04-16 14:03:06 UTC; windows
Archs: x64
