{
  "_id": "6a1971e4acfb0bcc41dee073",
  "Package": "ASpli",
  "Type": "Package",
  "Title": "Analysis of Alternative Splicing Using RNA-Seq",
  "Version": "2.23.0",
  "Date": "2024-03-22",
  "Author": "Estefania Mancini, Andres Rabinovich, Javier Iserte, Marcelo\nYanovsky and Ariel Chernomoretz",
  "License": "GPL",
  "biocViews": "ImmunoOncology, GeneExpression, Transcription,\nAlternativeSplicing, Coverage, DifferentialExpression,\nDifferentialSplicing, TimeCourse, RNASeq, GenomeAnnotation,\nSequencing, Alignment",
  "Description": "Integrative pipeline for the analysis of alternative\nsplicing using RNAseq.",
  "Maintainer": "Ariel Chernomoretz <algo107@gmail.com>",
  "Config/pak/sysreqs": "cmake libglpk-dev make libbz2-dev libicu-dev\nlibjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:43:57 UTC",
  "RemoteUrl": "https://github.com/bioc/ASpli",
  "RemoteRef": "HEAD",
  "RemoteSha": "ccb8e28be3a0a941f8adcaf533d42a9dd95a3f27",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 08:46:17 UTC",
    "User": "root"
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  "MD5sum": "ce58a9489e065f317798f125896fb357",
  "_user": "bioc",
  "_type": "src",
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  "_created": "2026-05-29T08:46:17.000Z",
  "_published": "2026-05-29T11:00:52.125Z",
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    "error": 4,
    "warning": 6,
    "note": 19
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26627323937",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/ASpli",
  "_commit": {
    "id": "ccb8e28be3a0a941f8adcaf533d42a9dd95a3f27",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380237
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  "_maintainer": {
    "name": "Ariel Chernomoretz",
    "email": "algo107@gmail.com",
    "login": "achernom",
    "description": "",
    "uuid": 12385672
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  "_registered": true,
  "_dependencies": [
    {
      "package": "methods",
      "role": "Depends"
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      "package": "stats",
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      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "GenomicFeatures",
      "role": "Imports"
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    {
      "package": "BiocGenerics",
      "role": "Imports"
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    {
      "package": "IRanges",
      "role": "Imports"
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    {
      "package": "GenomicAlignments",
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      "package": "Gviz",
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      "package": "Rsamtools",
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      "package": "grid",
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    },
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      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "pbmcapply",
      "role": "Imports"
    },
    {
      "package": "txdbmaker",
      "role": "Imports"
    }
  ],
  "_owner": "bioc",
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  "_usedby": 1,
  "_updates": [
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      "week": "2025-44",
      "n": 2
    },
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  "_tags": [],
  "_bioc": [
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      "branch": "devel",
      "version": "2.23.0",
      "bioc": "3.24"
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    {
      "branch": "release",
      "version": "2.22.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "geneexpression",
    "transcription",
    "alternativesplicing",
    "coverage",
    "differentialexpression",
    "differentialsplicing",
    "timecourse",
    "rnaseq",
    "genomeannotation",
    "sequencing",
    "alignment"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 546,
    "source": "https://www.bioconductor.org/packages/stats/bioc/ASpli"
  },
  "_mentions": 4,
  "_searchresults": 47,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/ASpli.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "altPSI",
    "altPSI<-",
    "anchorbased",
    "anchorbased<-",
    "anchorc",
    "anchorc<-",
    "anchorj",
    "anchorj<-",
    "AsDiscover",
    "aspliASexample",
    "aspliBamsExample",
    "aspliCountsExample",
    "aspliDUexample1",
    "aspliDUexample2",
    "aspliExampleBamList",
    "aspliExampleGTF",
    "aspliFeaturesExample",
    "aspliJunctionDUexample",
    "aspliTargetsExample",
    "binbased",
    "binbased<-",
    "binGenome",
    "binsDU",
    "binsDU<-",
    "condition.order",
    "containsGenesAndBins",
    "containsJunctions",
    "countsb",
    "countsb<-",
    "countse1i",
    "countse1i<-",
    "countsg",
    "countsg<-",
    "countsie2",
    "countsie2<-",
    "countsj",
    "countsj<-",
    "DUreport",
    "DUreport.norm",
    "DUreport.offset",
    "DUreportBinSplice",
    "esPSI",
    "esPSI<-",
    "exportIntegratedSignals",
    "exportSplicingReports",
    "featuresb",
    "featuresb<-",
    "featuresg",
    "featuresg<-",
    "featuresj",
    "featuresj<-",
    "filterDU",
    "filters",
    "filters<-",
    "filterSignals",
    "gbCounts",
    "gbDUreport",
    "genesDE",
    "genesDE<-",
    "getConditions",
    "integrateSignals",
    "irPIR",
    "irPIR<-",
    "jalt",
    "jalt<-",
    "jCounts",
    "jDUreport",
    "jes",
    "jes<-",
    "jir",
    "jir<-",
    "joint",
    "joint<-",
    "junctionDUreport",
    "junctionsDU",
    "junctionsDU<-",
    "junctionsPIR",
    "junctionsPIR<-",
    "junctionsPJU",
    "junctionsPJU<-",
    "loadBAM",
    "localebased",
    "localebased<-",
    "localec",
    "localec<-",
    "localej",
    "localej<-",
    "mergeBinDUAS",
    "plotBins",
    "plotGenomicRegions",
    "rds",
    "rdsb",
    "rdsb<-",
    "rdsg",
    "rdsg<-",
    "readCounts",
    "show",
    "signals",
    "signals<-",
    "splicingReport",
    "subset",
    "subsetBams",
    "subsetTargets",
    "targets",
    "transcriptExons",
    "transcriptExons<-",
    "writeAll",
    "writeAS",
    "writeCounts",
    "writeDU",
    "writeJDU",
    "writeRds",
    "writeSplicingReport"
  ],
  "_help": [
    {
      "page": "ASpli-package",
      "title": "Analysis of Alternative Splicing Using RNAseq",
      "topics": [
        "ASpli-package",
        "ASpli"
      ]
    },
    {
      "page": "acc_AS",
      "title": "Accessors for ASpliAS object",
      "topics": [
        "altPSI",
        "altPSI<-",
        "esPSI",
        "esPSI<-",
        "irPIR",
        "irPIR<-",
        "joint",
        "joint<-",
        "junctionsPIR",
        "junctionsPIR<-",
        "junctionsPJU",
        "junctionsPJU<-"
      ]
    },
    {
      "page": "ASpli-deprecated",
      "title": "Deprecated functions in package 'ASpli'",
      "topics": [
        "ASpli-deprecated"
      ]
    },
    {
      "page": "ASpliAS-class",
      "title": "Class '\"ASpliAS\"'",
      "topics": [
        "altPSI,ASpliAS-method",
        "altPSI<-,ASpliAS,data.frame-method",
        "ASpliAS",
        "ASpliAS-class",
        "esPSI,ASpliAS-method",
        "esPSI<-,ASpliAS,data.frame-method",
        "irPIR,ASpliAS-method",
        "irPIR<-,ASpliAS,data.frame-method",
        "jDUreport,ASpliAS-method",
        "joint,ASpliAS-method",
        "joint<-,ASpliAS,data.frame-method",
        "junctionsPIR,ASpliAS-method",
        "junctionsPIR<-,ASpliAS,data.frame-method",
        "junctionsPJU,ASpliAS-method",
        "junctionsPJU<-,ASpliAS,data.frame-method",
        "subset,ASpliAS-method",
        "writeAS,ASpliAS-method"
      ]
    },
    {
      "page": "ASpliCounts",
      "title": "Class '\"ASpliCounts\"'",
      "topics": [
        "ASpliCounts"
      ]
    },
    {
      "page": "ASpliCounts-class",
      "title": "Class '\"ASpliCounts\"'",
      "topics": [
        "AsDiscover,ASpliCounts-method",
        "ASpliCounts-class",
        "condition.order,ASpliCounts-method",
        "countsb,ASpliCounts-method",
        "countsb<-,ASpliCounts,data.frame-method",
        "countse1i,ASpliCounts-method",
        "countse1i<-,ASpliCounts,data.frame-method",
        "countsg,ASpliCounts-method",
        "countsg<-,ASpliCounts,data.frame-method",
        "countsie2,ASpliCounts-method",
        "countsie2<-,ASpliCounts,data.frame-method",
        "countsj,ASpliCounts-method",
        "countsj<-,ASpliCounts,data.frame-method",
        "DUreport,ASpliCounts-method",
        "DUreport.norm,ASpliCounts-method",
        "DUreport.offset,ASpliCounts-method",
        "DUreportBinSplice,ASpliCounts-method",
        "gbDUreport,ASpliCounts-method",
        "jCounts,ASpliCounts-method",
        "junctionDUreport,ASpliCounts-method",
        "plotBins,ASpliCounts-method",
        "rds,ASpliCounts-method",
        "rdsb,ASpliCounts-method",
        "rdsb<-,ASpliCounts,data.frame-method",
        "rdsg,ASpliCounts-method",
        "rdsg<-,ASpliCounts,data.frame-method",
        "subset,ASpliCounts-method",
        "targets,ASpliCounts-method",
        "targets<-,ASpliCounts,data.frame-method",
        "writeAll,ASpliCounts-method",
        "writeCounts,ASpliCounts-method",
        "writeRds,ASpliCounts-method"
      ]
    },
    {
      "page": "ASpliDU-class",
      "title": "Class '\"ASpliDU\"'",
      "topics": [
        "ASpliDU",
        "ASpliDU-class",
        "binsDU,ASpliDU-method",
        "binsDU<-,ASpliDU-method",
        "containsGenesAndBins,ASpliDU-method",
        "containsJunctions,ASpliDU-method",
        "filterDU,ASpliDU-method",
        "genesDE,ASpliDU-method",
        "genesDE<-,ASpliDU,data.frame-method",
        "junctionsDU,ASpliDU-method",
        "junctionsDU<-,ASpliDU,data.frame-method",
        "mergeBinDUAS,ASpliDU,ASpliAS-method",
        "splicingReport,ASpliDU-method",
        "writeDU,ASpliDU-method"
      ]
    },
    {
      "page": "ASpliFeatures-class",
      "title": "Class '\"ASpliFeatures\"'",
      "topics": [
        "ASpliFeatures-class",
        "featuresb,ASpliFeatures-method",
        "featuresb<-,ASpliFeatures,GRanges-method",
        "featuresg,ASpliFeatures-method",
        "featuresg<-,ASpliFeatures,GRangesList-method",
        "featuresj,ASpliFeatures-method",
        "featuresj<-,ASpliFeatures,GRanges-method",
        "gbCounts,ASpliFeatures-method",
        "plotGenomicRegions,ASpliFeatures-method",
        "readCounts,ASpliFeatures-method",
        "transcriptExons,ASpliFeatures-method",
        "transcriptExons<-,ASpliFeatures,GRangesList-method"
      ]
    },
    {
      "page": "ASpliIntegratedSignals-class",
      "title": "Class '\"ASpliIntegratedSignals\"'",
      "topics": [
        "ASpliIntegratedSignals",
        "ASpliIntegratedSignals-class",
        "exportIntegratedSignals,ASpliIntegratedSignals-method",
        "filters,ASpliIntegratedSignals-method",
        "filters<-,ASpliIntegratedSignals,data.frame-method",
        "show,ASpliIntegratedSignals-method",
        "signals,ASpliIntegratedSignals-method",
        "signals<-,ASpliIntegratedSignals,data.frame-method",
        "splicingReport,ASpliIntegratedSignals-method",
        "writeIntegratedSignals,ASpliIntegratedSignals-method"
      ]
    },
    {
      "page": "ASpliJDU-class",
      "title": "Class '\"ASpliJDU\"'",
      "topics": [
        "anchorc,ASpliJDU-method",
        "anchorc<-,ASpliJDU,data.frame-method",
        "anchorj,ASpliJDU-method",
        "anchorj<-,ASpliJDU,data.frame-method",
        "ASpliJDU",
        "ASpliJDU-class",
        "jalt,ASpliJDU-method",
        "jalt<-,ASpliJDU,data.frame-method",
        "jDUreport,ASpliJDU-method",
        "jes,ASpliJDU-method",
        "jes<-,ASpliJDU,data.frame-method",
        "jir,ASpliJDU-method",
        "jir<-,ASpliJDU,data.frame-method",
        "localec,ASpliJDU-method",
        "localec<-,ASpliJDU,data.frame-method",
        "localej,ASpliJDU-method",
        "localej<-,ASpliJDU,data.frame-method",
        "show,ASpliJDU-method",
        "writeJDU,ASpliJDU-method"
      ]
    },
    {
      "page": "ASpliSplicingReport-class",
      "title": "Class '\"ASpliSplicingReport\"'",
      "topics": [
        "anchorbased,ASpliSplicingReport-method",
        "anchorbased<-,ASpliSplicingReport,data.frame-method",
        "ASpliSplicingReport",
        "ASpliSplicingReport-class",
        "binbased,ASpliSplicingReport-method",
        "binbased<-,ASpliSplicingReport,data.frame-method",
        "exportSplicingReports,ASpliSplicingReport-method",
        "filterSignals,ASpliSplicingReport-method",
        "integrateSignals,ASpliSplicingReport-method",
        "localebased,ASpliSplicingReport-method",
        "localebased<-,ASpliSplicingReport,data.frame-method",
        "show,ASpliSplicingReport-method",
        "splicingReport,ASpliSplicingReport-method",
        "writeSplicingReport,ASpliSplicingReport-method"
      ]
    },
    {
      "page": "binGenome",
      "title": "Feature coordinates extraction",
      "topics": [
        "binGenome"
      ]
    },
    {
      "page": "binGenome-methods",
      "title": "Feature coordinates extraction",
      "topics": [
        "binGenome,TxDb-method",
        "binGenome-methods"
      ]
    },
    {
      "page": "acc_counts",
      "title": "Accessors for ASpliCounts object",
      "topics": [
        "condition.order",
        "countsb",
        "countsb<-",
        "countse1i",
        "countse1i<-",
        "countsg",
        "countsg<-",
        "countsie2",
        "countsie2<-",
        "countsj",
        "countsj<-",
        "rdsb",
        "rdsb<-",
        "rdsg",
        "rdsg<-",
        "targets"
      ]
    },
    {
      "page": "acc_DU",
      "title": "Accessors for ASpliDU object",
      "topics": [
        "binsDU",
        "binsDU<-",
        "genesDE",
        "genesDE<-",
        "junctionsDU",
        "junctionsDU<-"
      ]
    },
    {
      "page": "DUreport",
      "title": "Differential gene expression and differential bin usage estimation",
      "topics": [
        "DUreport"
      ]
    },
    {
      "page": "DUreport.norm",
      "title": "Differential gene expression and differential bin usage estimation",
      "topics": [
        "DUreport.norm"
      ]
    },
    {
      "page": "DUreport.offset",
      "title": "Differential gene expression and differential bin usage estimation",
      "topics": [
        "DUreport.offset"
      ]
    },
    {
      "page": "DUreportBinSplice-method",
      "title": "Differential gene expression and differential bin usage estimation",
      "topics": [
        "DUreportBinSplice"
      ]
    },
    {
      "page": "containsJunctions-function",
      "title": "Examine ASpliDU objects",
      "topics": [
        "containsGenesAndBins",
        "containsJunctions"
      ]
    },
    {
      "page": "example_data",
      "title": "Example Aspli objects",
      "topics": [
        "aspliASexample",
        "aspliBamsExample",
        "aspliCountsExample",
        "aspliDUexample1",
        "aspliDUexample2",
        "aspliExampleBamList",
        "aspliExampleGTF",
        "aspliFeaturesExample",
        "aspliJunctionDUexample",
        "aspliTargetsExample"
      ]
    },
    {
      "page": "exportIntegratedSignals",
      "title": "Export integrated signals.",
      "topics": [
        "exportIntegratedSignals"
      ]
    },
    {
      "page": "exportSplicingReports",
      "title": "Export splicing reports",
      "topics": [
        "exportSplicingReports"
      ]
    },
    {
      "page": "acc_features",
      "title": "Accessors for ASpliFeatures object",
      "topics": [
        "featuresb",
        "featuresb<-",
        "featuresg",
        "featuresg<-",
        "featuresj",
        "featuresj<-",
        "transcriptExons",
        "transcriptExons<-"
      ]
    },
    {
      "page": "filterDU-method",
      "title": "Filtering ASpliDU objects",
      "topics": [
        "filterDU"
      ]
    },
    {
      "page": "filterSignals",
      "title": "Filter signals",
      "topics": [
        "filterSignals"
      ]
    },
    {
      "page": "gbCounts",
      "title": "Summarize read overlaps",
      "topics": [
        "gbCounts",
        "readCounts"
      ]
    },
    {
      "page": "gbDUreport-method",
      "title": "Differential gene expression and differential bin usage estimation",
      "topics": [
        "gbDUreport"
      ]
    },
    {
      "page": "getConditions-function",
      "title": "Retrieve condition names from a targets data frame.",
      "topics": [
        "getConditions"
      ]
    },
    {
      "page": "acc_is",
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