{ "_id": "6a196762acfb0bcc41de7d2f", "Package": "casper", "Version": "2.47.0", "Date": "2026-03-12", "Title": "Characterization of Alternative Splicing Based on Paired-End\nReads", "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 ", "Description": "Infer alternative splicing from paired-end RNA-seq data.\nThe model is based on counting paths across exons, rather than\npairwise exon connections, and estimates the fragment size and\nstart distributions non-parametrically, which improves\nestimation precision.", "License": "GPL (>=2)", "LazyLoad": "yes", "Collate": "GenericDefs.R ClassDefinitions.R asymmetryCheck.R calcDenovo.R\ncalcExp.R casperVignettes.R createDenovoGenome.R genePlot.R\ngetDistrs.R getRoc.R denovoExpr.R makeTranscriptDbFromGFF.R\nmergeBatches.R mergeExp.R modelPrior.R pathCounts.R\nprobNonEquiv.R procBam.R procGenome.R qqnormGenomeWide.R\nrelexprByGene.R rmShortInserts.R simMultSamples.R simPost.R\nsimReads.R splitGenomeByLength.R truncnorm.R wrapKnown.R\nchecks.R wrapDenovo.R", "biocViews": "ImmunoOncology, GeneExpression, DifferentialExpression,\nTranscription, RNASeq, Sequencing", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-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": { "Date": "2026-05-29 08:30:23 UTC", "User": "root" }, "Author": "David Rossell [aut, cre],\nCamille Stephan-Otto [aut],\nManuel 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chromosome for a given Entrez, transcript or island id.", "topics": [ "getChr", "getChr,character,missing,missing,annotatedGenome-method", "getChr,missing,character,missing,annotatedGenome-method", "getChr,missing,missing,character,annotatedGenome-method", "getChr,missing,missing,missing,annotatedGenome-method", "getChr-method", "getIsland", "getIsland,character,missing,annotatedGenome-method", "getIsland,missing,character,annotatedGenome-method" ] }, { "page": "getNreads", "title": "Get total number of paths in each island from a pathCounts object.", "topics": [ "getNreads", "getNreads,pathCounts-method" ] }, { "page": "getReads", "title": "getReads returns the reads stored in a 'procBam' object.", "topics": [ "getReads", "getReads,procBam-method" ] }, { "page": "getRoc", "title": "Operating characteristics of differential expression analysis", "topics": [ "getRoc", "getRoc,logical,logical-method", "getRoc,matrix,matrix-method", "getRoc,numeric,numeric-method" ] }, { "page": "hg19DB", "title": "Subset of human genome (UCSC hg19 version)", "topics": [ "hg19DB" ] }, { "page": "K562.r1l1", "title": "Toy RNA-seq data from RGASP project.", "topics": [ "K562.r1l1" ] }, { "page": "mergeBatches", "title": "Merge two ExpressionSet objects by doing quantile normalization and computing partial residuals (i.e. substracting group mean expression in each batch). As currently implemented the method is only valid for balanced designs, e.g. each batch has the same number of samples per group.", "topics": [ "mergeBatches", "mergeBatches,ExpressionSet,ExpressionSet-method", "mergeBatches,ExpressionSet,simulatedSamples-method" ] }, { "page": "mergeExp", "title": "Merge splicing variant expression from multiple samples", "topics": [ "mergeExp" ] }, { "page": "modelPrior", "title": "Set prior distribution on expressed splicing variants.", "topics": [ "modelPrior" ] }, { "page": "modelPriorAS-class", "title": "Class \"modelPriorAS\"", "topics": [ "coef,modelPriorAS,ANY,ANY,ANY-method", "coef,modelPriorAS-method", "modelPriorAS-class", "show,modelPriorAS-method", "[,modelPriorAS,ANY,ANY,ANY-method" ] }, { "page": "pathCounts", "title": "Compute exon path counts", "topics": [ "pathCounts", "pathCounts,list-method", "pathCounts,procBam-method", "pathCounts-method" ] }, { "page": "pathCounts-class", "title": "Class \"pathCounts\"", "topics": [ "pathCounts-class", "show,pathCounts-method" ] }, { "page": "plot-methods", "title": "Plot estimated read start and fragment length distributions.", "topics": [ "lines", "lines,readDistrs-method", "plot", "plot,readDistrs,ANY-method", "plot,readDistrsList,ANY-method" ] }, { "page": "plotExpr", "title": "Plot inferred gene structure and expression.", "topics": [ "plotExpr", "plotExpr,denovoGeneExpr-method", "plotExpr-methods" ] }, { "page": "plotPriorAS", "title": "Plot prior distribution on set of expressed variants (i.e. the model space).", "topics": [ "plotPriorAS", "plotPriorAS,modelPriorAS-method", "plotPriorAS-methods" ] }, { "page": "probNonEquiv", "title": "'probNonEquiv' performs a Bayesian hypothesis test for equivalence between group means. It returns the posterior probability that |mu1-mu2|>logfc. 'pvalTreat' is a wrapper to 'treat' in package 'limma', which returns P-values for the same hypothesis test.", "topics": [ "probNonEquiv", "probNonEquiv,ExpressionSet-method", "probNonEquiv,list-method", "pvalTreat", "pvalTreat,ExpressionSet-method", "pvalTreat,list-method" ] }, { "page": "procBam", "title": "Process BAM object", "topics": [ "procBam", "procBam,ANY-method", "procBam,list,logical,integer,logical,character-method", "procBam,list,logical,integer,logical,missing-method", "procBam,list,logical,integer,missing,missing-method", "procBam,list,logical,missing,logical,missing-method", "procBam,list,logical,missing,missing,missing-method", "procBam,list,missing,integer,logical,missing-method", "procBam,list,missing,integer,missing,missing-method", "procBam,list,missing,missing,logical,missing-method", "procBam,list,missing,missing,missing,missing-method", "procBam,list,missing,numeric,missing,missing-method", "procBam-method" ] }, { "page": "procBam-class", "title": "Class 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