{
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  "Package": "SpliceWiz",
  "Title": "interactive analysis and visualization of alternative splicing\nin R",
  "Version": "1.15.2",
  "Date": "2026-10-06",
  "Authors@R": "c(person(\"Alex Chit Hei\", \"Wong\", email=\"alexchwong.github@gmail.com\", \nrole=c(\"aut\", \"cre\", \"cph\")),\nperson(\"Ulf\", \"Schmitz\", role=c(\"ctb\")),\nperson(\"William\", \"Ritchie\", role=c(\"cph\")))",
  "Description": "The analysis and visualization of alternative splicing\n(AS) events from RNA sequencing data remains challenging.\nSpliceWiz is a user-friendly and performance-optimized R\npackage for AS analysis, by processing alignment BAM files to\nquantify read counts across splice junctions, IRFinder-based\nintron retention quantitation, and supports novel splicing\nevent identification. We introduce a novel visualization for AS\nusing normalized coverage, thereby allowing visualization of\ndifferential AS across conditions. SpliceWiz features a\nshiny-based GUI facilitating interactive data exploration of\nresults including gene ontology enrichment. It is performance\noptimized with multi-threaded processing of BAM files and a new\nCOV file format for fast recall of sequencing coverage.\nOverall, SpliceWiz streamlines AS analysis, enabling reliable\nidentification of functionally relevant AS events for further\ncharacterization.",
  "License": "MIT + file LICENSE",
  "SystemRequirements": "C++11, GNU make",
  "Collate": "AllImports.R RcppExports.R zzz.R AllClasses.R AllGenerics.R\nASEFilter-methods.R NxtSE-methods.R globals.R ggplot_themes.R\nexample_data.R wrappers.R make_plot_data.R Coverage.R\ncovPlotly-methods.R covDataObject-methods.R\ncovPlotObject-methods.R plotCoverage.R utils.R File_finders.R\nBuildRef_GO.R BuildRef.R ViewRef.R STAR_utils.R Mappability.R\nProcessBAM_docs.R ProcessBAM.R CollateData.R MakeSE.R Filters.R\nASE-methods.R ASE-GLM-edgeR.R dash_filterModules.R\ndash_globals.R dash_settings.R dash_ref_new_ui.R\ndash_ref_new_server.R dash_expr_ui.R dash_expr_server.R\ndash_QC.R dash_filters.R dash_DE_ui.R dash_DE_server.R\ndash_vis_ui.R dash_vis_server.R dash_cov_ui.R dash_cov_server.R\ndash_GO_ui.R dash_GO_server.R dash_ui.R dash_server.R dash.R\nSpliceWiz-package.R",
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  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, Transcriptomics, RNASeq, AlternativeSplicing,\nCoverage, DifferentialSplicing, DifferentialExpression, GUI,\nSequencing",
  "URL": "https://github.com/alexchwong/SpliceWiz",
  "BugReports": "https://support.bioconductor.org/",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-10-05 22:48:31 UTC",
  "RemoteUrl": "https://github.com/bioc/SpliceWiz",
  "RemoteRef": "HEAD",
  "RemoteSha": "8b6b35a161cf6e6f51b394b737d4d43c0efee87b",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-11-01 14:25:11 UTC",
    "User": "root"
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  "Author": "Alex Chit Hei Wong [aut, cre, cph],\nUlf Schmitz [ctb],\nWilliam Ritchie [cph]",
  "Maintainer": "Alex Chit Hei Wong <alexchwong.github@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "SpliceWiz_1.15.2.tar.gz",
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  "_expires": "2027-02-09T18:12:25.000Z",
  "_created": "2026-11-01T14:25:11.000Z",
  "_published": "2026-11-01T18:12:27.064Z",
  "_upstream": "https://github.com/bioc/SpliceWiz",
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  "_rbuild": "4.6.2",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
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    "extra/readme.html",
    "extra/readme.md",
    "extra/SpliceWiz.html",
    "LICENSE"
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  "_homeurl": "https://github.com/alexchwong/splicewiz",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addPSI_edgeR",
    "applyFilters",
    "ASE_DESeq",
    "ASE_DoubleExpSeq",
    "ASE_edgeR",
    "ASE_edgeR_timeseries",
    "ASE_limma",
    "ASE_limma_timeseries",
    "ASEFilter",
    "assay",
    "assay<-",
    "assayNames",
    "assayNames<-",
    "assays",
    "assays<-",
    "BAM2COV",
    "buildFullRef",
    "buildRef",
    "calculateMappability",
    "cbind",
    "coerce",
    "colData",
    "colData<-",
    "collateData",
    "condition",
    "coord2GR",
    "covfile",
    "covfile<-",
    "down_exc",
    "down_exc<-",
    "down_inc",
    "down_inc<-",
    "extract_gene_ids_for_GO",
    "findBAMS",
    "findFASTQ",
    "findSamples",
    "findSpliceWizOutput",
    "fitASE_edgeR",
    "fitASE_edgeR_custom",
    "generateSyntheticReads",
    "getAvailableGO",
    "getCoverage",
    "getCoverage_DF",
    "getCoverageBins",
    "getCoverageData",
    "getCoverageRegions",
    "getDefaultFilters",
    "getExonRanges",
    "getGenomeData",
    "getNonPolyARef",
    "getPlotObject",
    "getResources",
    "goASE",
    "goGenes",
    "isCOV",
    "junc_counts",
    "junc_counts_uns",
    "junc_gr",
    "junc_PSI",
    "makeMatrix",
    "makeMeanPSI",
    "makeSE",
    "plotAnnoTrack",
    "plotCoverage",
    "plotGenome",
    "plotGO",
    "plotView",
    "processBAM",
    "rbind",
    "realize_NxtSE",
    "ref",
    "row_gr",
    "rowData",
    "rowData<-",
    "runFilter",
    "sampleQC",
    "sampleQC<-",
    "setResolution",
    "setSWthreads",
    "showEvents",
    "showExons",
    "sourcePath",
    "spliceWiz",
    "SpliceWiz_example_bams",
    "SpliceWiz_example_NxtSE",
    "STAR_alignExperiment",
    "STAR_alignReads",
    "STAR_buildGenome",
    "STAR_buildRef",
    "STAR_loadGenomeGTF",
    "STAR_mappability",
    "STAR_version",
    "subset_EventNames_by_GO",
    "testASE_edgeR",
    "theme_white",
    "theme_white_legend",
    "theme_white_legend_plot_track",
    "tracks",
    "up_exc",
    "up_exc<-",
    "up_inc",
    "up_inc<-",
    "update_NxtSE",
    "viewASE",
    "viewExons",
    "viewGenes",
    "viewGO",
    "viewIntrons",
    "viewIR",
    "viewIR_NMD",
    "viewProteins",
    "viewTranscripts"
  ],
  "_help": [
    {
      "page": "SpliceWiz-package",
      "title": "SpliceWiz: efficient and precise alternative splicing analysis in R",
      "topics": [
        "SpliceWiz-package",
        "SpliceWiz"
      ]
    },
    {
      "page": "ASE-GLM-edgeR",
      "title": "Using Generalised linear models (GLMs) to analyse differential ASEs using edgeR",
      "topics": [
        "addPSI_edgeR",
        "ASE-GLM-edgeR",
        "fitASE_edgeR",
        "fitASE_edgeR_custom",
        "testASE_edgeR"
      ]
    },
    {
      "page": "ASE-methods",
      "title": "Differential Alternative Splicing Event analysis",
      "topics": [
        "ASE-methods",
        "ASE_DESeq",
        "ASE_DoubleExpSeq",
        "ASE_edgeR",
        "ASE_edgeR_timeseries",
        "ASE_limma",
        "ASE_limma_timeseries"
      ]
    },
    {
      "page": "ASEFilter-class",
      "title": "SpliceWiz filters to remove low-confidence alternative splicing and intron retention events",
      "topics": [
        "ASEFilter",
        "ASEFilter-class"
      ]
    },
    {
      "page": "Build-Reference-methods",
      "title": "Builds reference files used by SpliceWiz",
      "topics": [
        "Build-Reference-methods",
        "buildFullRef",
        "buildRef",
        "getAvailableGO",
        "getNonPolyARef",
        "getResources"
      ]
    },
    {
      "page": "collateData",
      "title": "Collates a dataset from (processBAM) output files of individual samples",
      "topics": [
        "collateData"
      ]
    },
    {
      "page": "coord2GR",
      "title": "Converts genomic coordinates into a GRanges object",
      "topics": [
        "coord2GR"
      ]
    },
    {
      "page": "covDataObject-class",
      "title": "Container to hold raw data for SpliceWiz coverage plots",
      "topics": [
        "covDataObject-class",
        "getCoverageData",
        "getGenomeData",
        "plotAnnoTrack",
        "showEvents",
        "showEvents,covDataObject-method"
      ]
    },
    {
      "page": "Coverage",
      "title": "Calls SpliceWiz's C++ function to retrieve coverage from a COV file",
      "topics": [
        "Coverage",
        "getCoverage",
        "getCoverageBins",
        "getCoverageRegions",
        "getCoverage_DF"
      ]
    },
    {
      "page": "covPlotly-class",
      "title": "Container for plotly-based coverage plots",
      "topics": [
        "covPlotly-class",
        "getExonRanges",
        "getExonRanges,covPlotly-method",
        "setResolution",
        "setResolution,covPlotly-method",
        "showExons",
        "showExons,covPlotly-method"
      ]
    },
    {
      "page": "covPlotObject-class",
      "title": "Versatile coverage plots for SpliceWiz",
      "topics": [
        "condition",
        "condition,covPlotObject-method",
        "covPlotObject-class",
        "getPlotObject",
        "plotView",
        "tracks",
        "tracks,covPlotObject-method"
      ]
    },
    {
      "page": "example-SpliceWiz-data",
      "title": "SpliceWiz Example BAMs and NxtSE Experiment Object",
      "topics": [
        "example-SpliceWiz-data",
        "SpliceWiz_example_bams",
        "SpliceWiz_example_NxtSE"
      ]
    },
    {
      "page": "findSamples",
      "title": "Convenience Function to (recursively) find all files in a folder.",
      "topics": [
        "findBAMS",
        "findFASTQ",
        "findSamples",
        "findSpliceWizOutput"
      ]
    },
    {
      "page": "Gene-ontology-methods",
      "title": "Gene ontology (over-representation) analysis using enriched genes of top alternative splicing events",
      "topics": [
        "extract_gene_ids_for_GO",
        "Gene-ontology-methods",
        "goASE",
        "goGenes",
        "plotGO",
        "subset_EventNames_by_GO"
      ]
    },
    {
      "page": "Graphics-User-Interface",
      "title": "Launches the SpliceWiz Graphics User Interface (GUI) using Shiny Dashboard",
      "topics": [
        "Graphics-User-Interface",
        "GUI",
        "spliceWiz"
      ]
    },
    {
      "page": "isCOV",
      "title": "Validates the given file as a valid COV file",
      "topics": [
        "isCOV"
      ]
    },
    {
      "page": "make_plot_data",
      "title": "Construct data of percent-spliced-in (PSI) matrices and group-average PSIs",
      "topics": [
        "makeMatrix",
        "makeMeanPSI",
        "make_plot_data"
      ]
    },
    {
      "page": "makeSE",
      "title": "Imports a collated dataset into the R session as an NxtSE object",
      "topics": [
        "makeSE"
      ]
    },
    {
      "page": "Mappability-methods",
      "title": "Calculate low mappability genomic regions",
      "topics": [
        "calculateMappability",
        "generateSyntheticReads",
        "Mappability-methods"
      ]
    },
    {
      "page": "NxtSE-class",
      "title": "The NxtSE class",
      "topics": [
        "cbind,NxtSE-method",
        "coerce,SummarizedExperiment,NxtSE-method",
        "covfile",
        "covfile,NxtSE-method",
        "covfile<-",
        "covfile<-,NxtSE-method",
        "down_exc",
        "down_exc,NxtSE-method",
        "down_exc<-",
        "down_exc<-,NxtSE-method",
        "down_inc",
        "down_inc,NxtSE-method",
        "down_inc<-",
        "down_inc<-,NxtSE-method",
        "junc_counts",
        "junc_counts,NxtSE-method",
        "junc_counts_uns",
        "junc_counts_uns,NxtSE-method",
        "junc_gr",
        "junc_gr,NxtSE-method",
        "junc_PSI",
        "junc_PSI,NxtSE-method",
        "NxtSE",
        "NxtSE-class",
        "NxtSE-methods",
        "rbind,NxtSE-method",
        "realize_NxtSE",
        "realize_NxtSE,NxtSE-method",
        "ref",
        "ref,NxtSE-method",
        "row_gr",
        "row_gr,NxtSE-method",
        "sampleQC",
        "sampleQC,NxtSE-method",
        "sampleQC<-",
        "sampleQC<-,NxtSE-method",
        "sourcePath",
        "sourcePath,NxtSE-method",
        "update_NxtSE",
        "update_NxtSE,NxtSE-method",
        "up_exc",
        "up_exc,NxtSE-method",
        "up_exc<-",
        "up_exc<-,NxtSE-method",
        "up_inc",
        "up_inc,NxtSE-method",
        "up_inc<-",
        "up_inc<-,NxtSE-method",
        "[,NxtSE,ANY,ANY,ANY-method",
        "[<-,NxtSE,ANY,ANY,NxtSE-method"
      ]
    },
    {
      "page": "plotCoverage",
      "title": "RNA-seq Coverage Plots and Genome Tracks",
      "topics": [
        "plotCoverage",
        "plotGenome"
      ]
    },
    {
      "page": "processBAM",
      "title": "Runs the OpenMP/C++ based SpliceWiz algorithm",
      "topics": [
        "BAM2COV",
        "processBAM"
      ]
    },
    {
      "page": "Run_SpliceWiz_Filters",
      "title": "Filtering for IR and Alternative Splicing Events",
      "topics": [
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        "getDefaultFilters",
        "runFilter",
        "Run_SpliceWiz_Filters"
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    },
    {
      "page": "setSWthreads",
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      "topics": [
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      "page": "STAR-methods",
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      "topics": [
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        "STAR_alignReads",
        "STAR_buildGenome",
        "STAR_buildRef",
        "STAR_loadGenomeGTF",
        "STAR_mappability",
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        "theme_white_legend_plot_track"
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    {
      "page": "View-Reference-methods",
      "title": "View SpliceWiz Reference in read-able data frames",
      "topics": [
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        "viewASE",
        "viewExons",
        "viewGenes",
        "viewGO",
        "viewIntrons",
        "viewIR",
        "viewIR_NMD",
        "viewProteins",
        "viewTranscripts"
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