{
  "_id": "6a1b00a91d7bb097a09ffb41",
  "Package": "SGSeq",
  "Type": "Package",
  "Title": "Splice event prediction and quantification from RNA-seq data",
  "Version": "1.47.0",
  "Authors@R": "person(\"Leonard\", \"Goldstein\", email = \"ldgoldstein@gmail.com\", role = c(\"cre\", \"aut\"))",
  "Description": "SGSeq is a software package for analyzing splice events\nfrom RNA-seq data. Input data are RNA-seq reads mapped to a\nreference genome in BAM format. Genes are represented as a\nsplice graph, which can be obtained from existing annotation or\npredicted from the mapped sequence reads. Splice events are\nidentified from the graph and are quantified locally using\nstructurally compatible reads at the start or end of each\nsplice variant. The software includes functions for splice\nevent prediction, quantification, visualization and\ninterpretation.",
  "License": "Artistic-2.0",
  "LazyData": "yes",
  "VignetteBuilder": "knitr",
  "biocViews": "AlternativeSplicing, ImmunoOncology, RNASeq, Transcription",
  "RoxygenNote": "6.0.1",
  "Config/pak/sysreqs": "libglpk-dev make libbz2-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:40:03 UTC",
  "RemoteUrl": "https://github.com/bioc/SGSeq",
  "RemoteRef": "HEAD",
  "RemoteSha": "64bc43b8111bf2dc671c905c5cf888a28a987fe4",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:53:41 UTC",
    "User": "root"
  },
  "Author": "Leonard Goldstein [cre, aut]",
  "Maintainer": "Leonard Goldstein <ldgoldstein@gmail.com>",
  "MD5sum": "779297f43bcc543efd6bea8463cb7f32",
  "_user": "bioc",
  "_type": "src",
  "_file": "SGSeq_1.47.0.tar.gz",
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  "_sha256": "f3cdc024f4876c5a90585f046bf30c0ca493037a76f20fe5822ea4dea8a57dd0",
  "_created": "2026-05-30T09:53:41.000Z",
  "_published": "2026-05-30T15:22:17.546Z",
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677065998",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/SGSeq",
  "_commit": {
    "id": "64bc43b8111bf2dc671c905c5cf888a28a987fe4",
    "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",
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  "_maintainer": {
    "name": "Leonard Goldstein",
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    "login": "ldg21",
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    "uuid": 6200908
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  "_dependencies": [
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      "package": "R",
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      "package": "IRanges",
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      "package": "GenomicRanges",
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      "package": "Rsamtools",
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      "package": "SummarizedExperiment",
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      "package": "Seqinfo",
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      "package": "BSgenome.Hsapiens.UCSC.hg19",
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      "package": "TxDb.Hsapiens.UCSC.hg19.knownGene",
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  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 3,
  "_updates": [
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      "week": "2025-44",
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  "_tags": [],
  "_bioc": [
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      "branch": "devel",
      "version": "1.47.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.46.0",
      "bioc": "3.23"
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  ],
  "_topics": [
    "alternativesplicing",
    "immunooncology",
    "rnaseq",
    "transcription"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 754,
    "source": "https://www.bioconductor.org/packages/stats/bioc/SGSeq"
  },
  "_mentions": 14,
  "_searchresults": 52,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
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    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "analyzeFeatures",
    "analyzeVariants",
    "annotate",
    "closed3p",
    "closed3p<-",
    "closed3pEvent",
    "closed3pEvent<-",
    "closed5p",
    "closed5p<-",
    "closed5pEvent",
    "closed5pEvent<-",
    "convertToSGFeatures",
    "convertToTxFeatures",
    "counts",
    "counts<-",
    "eventID",
    "eventID<-",
    "exportFeatures",
    "featureID",
    "featureID<-",
    "featureID3p",
    "featureID3p<-",
    "featureID3pEvent",
    "featureID3pEvent<-",
    "featureID5p",
    "featureID5p<-",
    "featureID5pEvent",
    "featureID5pEvent<-",
    "findSGVariants",
    "FPKM",
    "FPKM<-",
    "from",
    "from<-",
    "geneID",
    "geneID<-",
    "geneName",
    "geneName<-",
    "getBamInfo",
    "getSGFeatureCounts",
    "getSGVariantCounts",
    "importTranscripts",
    "makeSGFeatureCounts",
    "makeVariantNames",
    "mergeTxFeatures",
    "plotCoverage",
    "plotFeatures",
    "plotSpliceGraph",
    "plotVariants",
    "predictTxFeatures",
    "predictVariantEffects",
    "processTerminalExons",
    "segmentID",
    "segmentID<-",
    "SGFeatureCounts",
    "SGFeatures",
    "SGVariantCounts",
    "SGVariants",
    "splice3p",
    "splice3p<-",
    "splice5p",
    "splice5p<-",
    "to",
    "to<-",
    "TxFeatures",
    "txName",
    "txName<-",
    "type",
    "type<-",
    "updateObject",
    "variantFreq",
    "variantFreq<-",
    "variantID",
    "variantID<-",
    "variantName",
    "variantName<-",
    "variantType",
    "variantType<-"
  ],
  "_datasets": [
    {
      "name": "gr",
      "title": "Example genomic region of interest",
      "object": "gr",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sgf_ann",
      "title": "Example splice graph features (annotation-based)",
      "object": "sgf_ann",
      "class": [
        "SGFeatures"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sgf_pred",
      "title": "Example splice graph features (predicted)",
      "object": "sgf_pred",
      "class": [
        "SGFeatures"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sgfc_ann",
      "title": "Example splice graph feature counts (annotation-based)",
      "object": "sgfc_ann",
      "class": [
        "SGFeatureCounts"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sgfc_pred",
      "title": "Example splice graph feature counts (predicted)",
      "object": "sgfc_pred",
      "class": [
        "SGFeatureCounts"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sgv_ann",
      "title": "Example splice variants (annotation-based)",
      "object": "sgv_ann",
      "class": [
        "SGVariants"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sgv_pred",
      "title": "Example splice variants (predicted)",
      "object": "sgv_pred",
      "class": [
        "SGVariants"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sgvc_ann",
      "title": "Example splice variant counts (annotated)",
      "object": "sgvc_ann",
      "class": [
        "SGVariantCounts"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sgvc_ann_from_bam",
      "title": "Example splice variant counts (annotated) from BAM files",
      "object": "sgvc_ann_from_bam",
      "class": [
        "SGVariantCounts"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sgvc_pred",
      "title": "Example splice variant counts (predicted)",
      "object": "sgvc_pred",
      "class": [
        "SGVariantCounts"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sgvc_pred_from_bam",
      "title": "Example splice variant counts (predicted) from BAM files",
      "object": "sgvc_pred_from_bam",
      "class": [
        "SGVariantCounts"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "si",
      "title": "Example sample information",
      "object": "si",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample_name",
        "file_bam",
        "paired_end",
        "read_length",
        "frag_length",
        "lib_size"
      ],
      "rows": 8,
      "table": true,
      "tojson": true
    },
    {
      "name": "tx",
      "title": "Example transcripts",
      "object": "tx",
      "class": [
        "CompressedGRangesList"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "txf_ann",
      "title": "Example transcript features (annotation-based)",
      "object": "txf_ann",
      "class": [
        "TxFeatures"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "txf_pred",
      "title": "Example transcript features (predicted)",
      "object": "txf_pred",
      "class": [
        "TxFeatures"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "analyzeFeatures",
      "title": "Analysis of splice graph features from BAM files",
      "topics": [
        "analyzeFeatures"
      ]
    },
    {
      "page": "analyzeVariants",
      "title": "Analysis of splice variants",
      "topics": [
        "analyzeVariants"
      ]
    },
    {
      "page": "annotate",
      "title": "Annotation with respect to transcript features",
      "topics": [
        "annotate"
      ]
    },
    {
      "page": "assays",
      "title": "Accessing and replacing assay data",
      "topics": [
        "assays",
        "counts,SGFeatureCounts-method",
        "counts,SGVariantCounts-method",
        "counts<-,SGFeatureCounts-method",
        "counts<-,SGVariantCounts-method",
        "FPKM",
        "FPKM,SGFeatureCounts-method",
        "FPKM,SGVariantCounts-method",
        "FPKM<-",
        "FPKM<-,SGFeatureCounts-method",
        "variantFreq",
        "variantFreq,SGVariantCounts-method",
        "variantFreq<-",
        "variantFreq<-,SGVariantCounts-method"
      ]
    },
    {
      "page": "convertToSGFeatures",
      "title": "Convert transcript features to splice graph features",
      "topics": [
        "convertToSGFeatures"
      ]
    },
    {
      "page": "convertToTxFeatures",
      "title": "Convert to TxFeatures object",
      "topics": [
        "convertToTxFeatures"
      ]
    },
    {
      "page": "exportFeatures",
      "title": "Export to BED format",
      "topics": [
        "exportFeatures"
      ]
    },
    {
      "page": "findSGVariants",
      "title": "Identify splice variants from splice graph",
      "topics": [
        "findSGVariants"
      ]
    },
    {
      "page": "getBamInfo",
      "title": "Obtain library information from BAM files",
      "topics": [
        "getBamInfo"
      ]
    },
    {
      "page": "getSGFeatureCounts",
      "title": "Compatible counts for splice graph features from BAM files",
      "topics": [
        "getSGFeatureCounts"
      ]
    },
    {
      "page": "getSGVariantCounts",
      "title": "Representative counts and frequency estimates for splice variants",
      "topics": [
        "getSGVariantCounts"
      ]
    },
    {
      "page": "importTranscripts",
      "title": "Import transcripts from GFF file",
      "topics": [
        "importTranscripts"
      ]
    },
    {
      "page": "makeSGFeatureCounts",
      "title": "Create 'SGFeatureCounts' object",
      "topics": [
        "makeSGFeatureCounts"
      ]
    },
    {
      "page": "mergeTxFeatures",
      "title": "Merge redundant features",
      "topics": [
        "mergeTxFeatures"
      ]
    },
    {
      "page": "plotCoverage",
      "title": "Plot read coverage and splice junction read counts",
      "topics": [
        "plotCoverage"
      ]
    },
    {
      "page": "plotFeatures",
      "title": "Plot splice graph and heatmap of expression values",
      "topics": [
        "plotFeatures"
      ]
    },
    {
      "page": "plotSpliceGraph",
      "title": "Plot splice graph",
      "topics": [
        "plotSpliceGraph"
      ]
    },
    {
      "page": "plotVariants",
      "title": "Plot splice graph and heatmap of splice variant frequencies",
      "topics": [
        "plotVariants"
      ]
    },
    {
      "page": "predictTxFeatures",
      "title": "Splice junction and exon prediction from BAM files",
      "topics": [
        "predictTxFeatures"
      ]
    },
    {
      "page": "predictVariantEffects",
      "title": "Predict the effect of splice variants on protein-coding transcripts",
      "topics": [
        "predictVariantEffects"
      ]
    },
    {
      "page": "processTerminalExons",
      "title": "Process predicted terminal exons",
      "topics": [
        "processTerminalExons"
      ]
    },
    {
      "page": "SGFeatureCounts",
      "title": "Splice graph feature counts",
      "topics": [
        "SGFeatureCounts"
      ]
    },
    {
      "page": "SGFeatures",
      "title": "Splice graph features",
      "topics": [
        "SGFeatures"
      ]
    },
    {
      "page": "SGVariantCounts",
      "title": "Splice graph variant counts",
      "topics": [
        "SGVariantCounts"
      ]
    },
    {
      "page": "SGVariants",
      "title": "Splice graph variants",
      "topics": [
        "SGVariants"
      ]
    },
    {
      "page": "slots",
      "title": "Accessing and replacing metadata columns",
      "topics": [
        "closed3p",
        "closed3p,SGVariantCounts-method",
        "closed3p,SGVariants-method",
        "closed3p<-",
        "closed3p<-,SGVariantCounts-method",
        "closed3p<-,SGVariants-method",
        "closed3pEvent",
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        "closed3pEvent<-",
        "closed3pEvent<-,SGVariantCounts-method",
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        "closed5p",
        "closed5p,SGVariantCounts-method",
        "closed5p,SGVariants-method",
        "closed5p<-",
        "closed5p<-,SGVariantCounts-method",
        "closed5p<-,SGVariants-method",
        "closed5pEvent",
        "closed5pEvent,SGVariantCounts-method",
        "closed5pEvent,SGVariants-method",
        "closed5pEvent<-",
        "closed5pEvent<-,SGVariantCounts-method",
        "closed5pEvent<-,SGVariants-method",
        "eventID",
        "eventID,SGVariantCounts-method",
        "eventID,SGVariants-method",
        "eventID<-",
        "eventID<-,SGVariantCounts-method",
        "eventID<-,SGVariants-method",
        "featureID",
        "featureID,Counts-method",
        "featureID,Paths-method",
        "featureID,SGFeatures-method",
        "featureID3p",
        "featureID3p,SGVariantCounts-method",
        "featureID3p,SGVariants-method",
        "featureID3p<-",
        "featureID3p<-,SGVariantCounts-method",
        "featureID3p<-,SGVariants-method",
        "featureID3pEvent",
        "featureID3pEvent,SGVariantCounts-method",
        "featureID3pEvent,SGVariants-method",
        "featureID3pEvent<-",
        "featureID3pEvent<-,SGVariantCounts-method",
        "featureID3pEvent<-,SGVariants-method",
        "featureID5p",
        "featureID5p,SGVariantCounts-method",
        "featureID5p,SGVariants-method",
        "featureID5p<-",
        "featureID5p<-,SGVariantCounts-method",
        "featureID5p<-,SGVariants-method",
        "featureID5pEvent",
        "featureID5pEvent,SGVariantCounts-method",
        "featureID5pEvent,SGVariants-method",
        "featureID5pEvent<-",
        "featureID5pEvent<-,SGVariantCounts-method",
        "featureID5pEvent<-,SGVariants-method",
        "featureID<-",
        "featureID<-,Counts-method",
        "featureID<-,Paths-method",
        "featureID<-,SGFeatures-method",
        "from,Paths-method",
        "from,SGVariantCounts-method",
        "from<-",
        "from<-,Paths-method",
        "from<-,SGVariantCounts-method",
        "geneID",
        "geneID,Counts-method",
        "geneID,Paths-method",
        "geneID,SGFeatures-method",
        "geneID<-",
        "geneID<-,Counts-method",
        "geneID<-,Paths-method",
        "geneID<-,SGFeatures-method",
        "geneName",
        "geneName,Counts-method",
        "geneName,Features-method",
        "geneName,Paths-method",
        "geneName<-",
        "geneName<-,Counts-method",
        "geneName<-,Features-method",
        "geneName<-,Paths-method",
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        "segmentID,Paths-method",
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      "source": "SGSeq.Rmd",
      "filename": "SGSeq.html",
      "title": "Splice event prediction and quantification from RNA-seq data",
      "author": "Leonard D Goldstein",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Preliminaries",
        "RNA transcripts and the TxFeatures class",
        "The splice graph and the SGFeatures class",
        "Splice graph analysis based on annotated transcripts",
        "Splice graph analysis based on de novo prediction",
        "Splice variant identification",
        "Splice variant quantification",
        "Splice variant interpretation",
        "Visualization",
        "Testing for differential splice variant usage",
        "Advanced usage",
        "Multi-core use and memory requirements",
        "Session information",
        "References"
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      "created": "2015-10-10 22:49:30",
      "modified": "2025-07-22 19:31:37",
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