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  "Package": "IsoformSwitchAnalyzeR",
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  "Title": "Identify, Annotate and Visualize Isoform Switches with\nFunctional Consequences from both short- and long-read RNA-seq\ndata",
  "Version": "2.13.0",
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  "Description": "Analysis of alternative splicing and isoform switches with\npredicted functional consequences (e.g. gain/loss of protein\ndomains etc.) from quantification of all types of RNA-seq\n(short/long) by tools such as Kallisto, Salmon, StringTie,\nTallon, IsoQuant etc.",
  "URL": "http://bioconductor.org/packages/IsoformSwitchAnalyzeR/",
  "BugReports": "https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues",
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  "Collate": "classes.R methods.R import_data.R test_isoform_switches.R\nanalyze_ORF.R analyze_external_sequence_analysis.R\nanalyze_switch_consequences.R isoform_plots.R\nplot_all_iso_switch.R high_level_functions.R tools.R\nanalyze_alternative_splicing.R",
  "biocViews": "GeneExpression, Transcription, AlternativeSplicing,\nDifferentialExpression, DifferentialSplicing, Visualization,\nStatisticalMethod, TranscriptomeVariant, BiomedicalInformatics,\nFunctionalGenomics, SystemsBiology, Transcriptomics, RNASeq,\nAnnotation, FunctionalPrediction, GenePrediction, DataImport,\nMultipleComparison, BatchEffect, ImmunoOncology",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:45:47 UTC",
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  "Author": "Kristoffer Vitting-Seerup [cre, aut] (ORCID:\n<https://orcid.org/0000-0002-6450-0608>),\nChunxu Han [ctb],\nJeroen Gilis [ctb] (ORCID: <https://orcid.org/0000-0001-8415-0943>),\nElena Iriondo Delgado [ctb]",
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    "analyzeAlternativeSplicing",
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    "extractConsequenceEnrichmentComparison",
    "extractConsequenceGenomeWide",
    "extractConsequenceSummary",
    "extractGeneExpression",
    "extractGenomeWideAnalysis",
    "extractSequence",
    "extractSplicingEnrichment",
    "extractSplicingEnrichmentComparison",
    "extractSplicingGenomeWide",
    "extractSplicingSummary",
    "extractSubCellShifts",
    "extractSwitchOverlap",
    "extractSwitchSummary",
    "extractTopSwitches",
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    "isoformSwitchAnalysisCombined",
    "isoformSwitchAnalysisPart1",
    "isoformSwitchAnalysisPart2",
    "isoformSwitchTestDEXSeq",
    "isoformSwitchTestSatuRn",
    "isoformToGeneExp",
    "isoformToIsoformFraction",
    "preFilter",
    "prepareSalmonFileDataFrame",
    "subsetSwitchAnalyzeRlist",
    "switchPlot",
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    "switchPlotIsoUsage",
    "switchPlotTopSwitches",
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      "title": "Example data for IsoformSwitchAnalyzeR",
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      "file": "exampleSwitchList.RData",
      "class": [
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      "fields": [],
      "table": false,
      "tojson": false
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      "title": "Example data for IsoformSwitchAnalyzeR",
      "object": "exampleSwitchListAnalyzed",
      "file": "exampleSwitchListAnalyzed.RData",
      "class": [
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      "table": false,
      "tojson": false
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      "name": "exampleSwitchListIntermediary",
      "title": "Example data for IsoformSwitchAnalyzeR",
      "object": "exampleSwitchListIntermediary",
      "file": "exampleSwitchListIntermediary.RData",
      "class": [
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      "table": false,
      "tojson": false
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      "title": "Add CDS from a GTF file to a switchAnalyzeRlist.",
      "topics": [
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    {
      "page": "analyzeAlternativSplicing",
      "title": "Analyse alternative splicing (including intron retention(s))",
      "topics": [
        "analyzeAlternativeSplicing",
        "analyzeIntronRetention"
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    },
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      "page": "analyzeCPAT",
      "title": "Import Result of External Sequence Analysis",
      "topics": [
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      "page": "analyzeCPC2",
      "title": "Import Result of External Sequence Analysis",
      "topics": [
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      "page": "analyzeDeepLoc2",
      "title": "Import Result of DeepLoc2 Analysis",
      "topics": [
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    {
      "page": "analyzeDeepTMHMM",
      "title": "Import Result of a DeepTMHMM analysis",
      "topics": [
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    },
    {
      "page": "analyzeIUPred2A",
      "title": "Import Result of IUPred2A or IUPred3 analysis",
      "topics": [
        "analyzeIUPred2A"
      ]
    },
    {
      "page": "analyzeNetSurfP3",
      "title": "Import Result of NetSurfP3 analysis",
      "topics": [
        "analyzeNetSurfP3"
      ]
    },
    {
      "page": "analyzeNovelIsoformORF",
      "title": "Prediction of Isoform Open Reading Frames.",
      "topics": [
        "analyzeNovelIsoformORF"
      ]
    },
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      "page": "analyzeORF",
      "title": "Prediction of Transcript Open Reading Frame.",
      "topics": [
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    {
      "page": "analyzePFAM",
      "title": "Import Result of PFAM analysis",
      "topics": [
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      "page": "analyzeSignalP",
      "title": "Import Result of SignalP Analysis",
      "topics": [
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    {
      "page": "analyzeSwitchConsequences",
      "title": "Analyze Consequences of Isoform Switches",
      "topics": [
        "analyzeSwitchConsequences"
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    {
      "page": "switchAnalyzeRlist",
      "title": "Create a switchAnalyzeRlist Object",
      "topics": [
        "createSwitchAnalyzeRlist",
        "switchAnalyzeRlist",
        "switchAnalyzeRlist-class"
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    {
      "page": "testData",
      "title": "Example data for IsoformSwitchAnalyzeR",
      "topics": [
        "exampleSwitchList",
        "exampleSwitchListAnalyzed",
        "exampleSwitchListIntermediary"
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    {
      "page": "exportToPairedGSEA",
      "title": "Export Data for pairedGSEA Analysis",
      "topics": [
        "exportToPairedGSEA"
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    },
    {
      "page": "extractConsequenceEnrichment",
      "title": "Analyze data for enrichment of specific consequences",
      "topics": [
        "extractConsequenceEnrichment"
      ]
    },
    {
      "page": "extractConsequenceEnrichmentComparison",
      "title": "Compare enrichment of specific consequences between comparisons",
      "topics": [
        "extractConsequenceEnrichmentComparison"
      ]
    },
    {
      "page": "extractGenomeWideAnalysis",
      "title": "Genome wide Analysis of Consequences due to isoform switching",
      "topics": [
        "extractConsequenceGenomeWide",
        "extractGenomeWideAnalysis"
      ]
    },
    {
      "page": "extractConsequenceSummary",
      "title": "Analyze Switch Consequences",
      "topics": [
        "extractConsequenceSummary"
      ]
    },
    {
      "page": "extractGeneExpression",
      "title": "Extract raw gene counts or abundances from a switchAnalyzeRlist object.",
      "topics": [
        "extractGeneExpression"
      ]
    },
    {
      "page": "extractSequence",
      "title": "Extract nucloetide (and amino acid) sequence of transcripts.",
      "topics": [
        "extractSequence"
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    },
    {
      "page": "extractSplicingEnrichment",
      "title": "Analyze data for enrichment of specific type of alternative splicing",
      "topics": [
        "extractSplicingEnrichment"
      ]
    },
    {
      "page": "extractSplicingEnrichmentComparison",
      "title": "Compare enrichment of specific type of alternative splicing between comparisons",
      "topics": [
        "extractSplicingEnrichmentComparison"
      ]
    },
    {
      "page": "extractGenomeWideSplicingAnalysis",
      "title": "Genome wide Analysis of alternative splicing",
      "topics": [
        "extractSplicingGenomeWide"
      ]
    },
    {
      "page": "extractSplicingSummary",
      "title": "Extracts alternative splicing summary",
      "topics": [
        "extractSplicingSummary"
      ]
    },
    {
      "page": "extractSubCellShifts",
      "title": "Global overview of sub-cellular location changes",
      "topics": [
        "extractSubCellShifts"
      ]
    },
    {
      "page": "extractSwitchOverlap",
      "title": "Visualize Switch Overlap",
      "topics": [
        "extractSwitchOverlap"
      ]
    },
    {
      "page": "extractSwitchSummary",
      "title": "Summarize Isoform Switches test Result.",
      "topics": [
        "extractSwitchSummary"
      ]
    },
    {
      "page": "extractTopSwitches",
      "title": "Extract Top Isoform Switches.",
      "topics": [
        "extractTopSwitches"
      ]
    },
    {
      "page": "importCufflinksGalaxyData",
      "title": "Import CuffDiff (Cufflinks) Data Into R",
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