Package: casper
Version: 2.47.0
Date: 2026-03-12
Title: Characterization of Alternative Splicing Based on Paired-End
        Reads
Authors@R: c(person(given = "David", family = "Rossell", role = c("aut", "cre"), email = "rosselldavid@gmail.com"), person(given = "Camille", family = "Stephan-Otto", role = "aut"), person(given = "Manuel", family = "Kroiss", role = "aut"), person(given = "Miranda", family = "Stobbe", role = "aut"), person(given = "Victor", family = "Pena", role = "aut"))
Maintainer: David Rossell <rosselldavid@gmail.com>
Depends: R (>= 3.6.0), Biobase, IRanges, methods, GenomicRanges
Imports: BiocGenerics (>= 0.31.6), coda, EBarrays, gaga, gtools,
        Seqinfo, GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer,
        S4Vectors (>= 0.9.25), sqldf, survival, txdbmaker, 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
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:37:14 UTC
RemoteUrl: https://github.com/bioc/casper
RemoteRef: HEAD
RemoteSha: 2471cc4deb01d422191faccc332d926cef3d528d
NeedsCompilation: yes
Packaged: 2026-05-29 08:30:23 UTC; root
Author: David Rossell [aut, cre],
  Camille Stephan-Otto [aut],
  Manuel Kroiss [aut],
  Miranda Stobbe [aut],
  Victor Pena [aut]
Built: R 4.6.0; x86_64-w64-mingw32; 2026-05-29 08:33:56 UTC; windows
Archs: x64
