{
  "_id": "6ad341e94bc68bd0bd9bdb8b",
  "Package": "OutSplice",
  "Type": "Package",
  "Title": "Comparison of Splicing Events between Tumor and Normal Samples",
  "Version": "1.13.0",
  "Authors@R": "c(person(\"Joseph\", \"Bendik\", role = \"aut\", comment = c(ORCID = \"0000-0003-0877-5639\")),\nperson(\"Sandhya\", \"Kalavacherla\", role = \"aut\", comment = c(ORCID = \"0000-0003-0485-9042\")),\nperson(\"Michael\", \"Considine\", role = \"aut\", comment = c(ORCID = \"0000-0002-8666-4857\")),\nperson(\"Bahman\", \"Afsari\", role = \"aut\", comment = c(ORCID = \"0000-0001-8717-7199\")),\nperson(\"Michael F.\", \"Ochs\", role = \"aut\"),\nperson(\"Joseph\", \"Califano\", role = \"aut\", comment = c(ORCID = \"0000-0002-4715-6761\")),\nperson(\"Daria A.\", \"Gaykalova\", role = \"aut\", comment = c(ORCID = \"0000-0001-5037-0147\")),\nperson(\"Elana\", \"Fertig\", role = \"aut\", comment = c(ORCID = \"0000-0003-3204-342X\")),\nperson(\"Theresa\", \"Guo\", email = \"twguo@health.ucsd.edu\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-1689-3275\")))",
  "Description": "An easy to use tool that can compare splicing events in\ntumor and normal tissue samples using either a user generated\nmatrix, or data from The Cancer Genome Atlas (TCGA). This\npackage generates a matrix of splicing outliers that are\nsignificantly over or underexpressed in tumors samples compared\nto normal denoted by chromosome location. The package also will\ncalculate the splicing burden in each tumor and characterize\nthe types of splicing events that occur.",
  "Encoding": "UTF-8",
  "License": "GPL-2",
  "VignetteBuilder": "knitr",
  "biocViews": "AlternativeSplicing, DifferentialExpression,\nDifferentialSplicing, GeneExpression, RNASeq, Software,\nVariantAnnotation",
  "BugReports": "https://github.com/GuoLabUCSD/OutSplice/issues",
  "URL": "https://github.com/GuoLabUCSD/OutSplice",
  "RoxygenNote": "7.2.3",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:00:42 UTC",
  "RemoteUrl": "https://github.com/bioc/OutSplice",
  "RemoteRef": "HEAD",
  "RemoteSha": "60d4ae860a4acd09106f01d4df4cc4a2da7459c0",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-17 09:28:28 UTC",
    "User": "root"
  },
  "Author": "Joseph Bendik [aut] (ORCID: <https://orcid.org/0000-0003-0877-5639>),\nSandhya Kalavacherla [aut] (ORCID:\n<https://orcid.org/0000-0003-0485-9042>),\nMichael Considine [aut] (ORCID:\n<https://orcid.org/0000-0002-8666-4857>),\nBahman Afsari [aut] (ORCID: <https://orcid.org/0000-0001-8717-7199>),\nMichael F. Ochs [aut],\nJoseph Califano [aut] (ORCID: <https://orcid.org/0000-0002-4715-6761>),\nDaria A. Gaykalova [aut] (ORCID:\n<https://orcid.org/0000-0001-5037-0147>),\nElana Fertig [aut] (ORCID: <https://orcid.org/0000-0003-3204-342X>),\nTheresa Guo [cre, aut] (ORCID: <https://orcid.org/0000-0002-1689-3275>)",
  "Maintainer": "Theresa Guo <twguo@health.ucsd.edu>",
  "_user": "bioc",
  "_type": "src",
  "_file": "OutSplice_1.13.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/70edfe0833fcba251096ee888d59f15e23406f5ce38f104ca753470fb1fa3614",
  "_filesize": 3938864,
  "_sha256": "70edfe0833fcba251096ee888d59f15e23406f5ce38f104ca753470fb1fa3614",
  "_expires": "2027-01-25T09:37:41.000Z",
  "_created": "2026-10-17T09:28:28.000Z",
  "_published": "2026-10-17T09:37:44.392Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39020925716",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 4
  },
  "_upstream": "https://github.com/bioc/OutSplice",
  "_commit": {
    "id": "60d4ae860a4acd09106f01d4df4cc4a2da7459c0",
    "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": 1777381242
  },
  "_maintainer": {
    "name": "Theresa Guo",
    "email": "twguo@health.ucsd.edu",
    "login": "theresaguo",
    "description": "",
    "uuid": 48133861,
    "orcid": "0000-0002-1689-3275"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 117363484128,
      "time": 205,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12097345615"
    },
    {
      "job": 117363484069,
      "time": 502,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12096459997"
    },
    {
      "job": 117363484117,
      "time": 395,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12097071796"
    },
    {
      "job": 117363484104,
      "time": 281,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12096996856"
    },
    {
      "job": 117363484155,
      "time": 235,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12097021007"
    },
    {
      "job": 117362458591,
      "time": 332,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12096404199"
    },
    {
      "job": 117363484091,
      "time": 180,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12096733213"
    },
    {
      "job": 117363484076,
      "time": 317,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12097385274"
    },
    {
      "job": 117363484115,
      "time": 312,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12096951275"
    },
    {
      "job": 117363484146,
      "time": 268,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12097171219"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3",
      "role": "Depends"
    },
    {
      "package": "AnnotationDbi",
      "version": ">= 1.60.0",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "version": ">= 1.49.0",
      "role": "Imports"
    },
    {
      "package": "GenomicFeatures",
      "version": ">= 1.50.2",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "version": ">= 2.32.0",
      "role": "Imports"
    },
    {
      "package": "org.Hs.eg.db",
      "version": ">= 3.16.0",
      "role": "Imports"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg19.knownGene",
      "version": ">= 3.2.2",
      "role": "Imports"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg38.knownGene",
      "version": ">= 3.16.0",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "version": ">= 0.36.0",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.13.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.12.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "alternativesplicing",
    "differentialexpression",
    "differentialsplicing",
    "geneexpression",
    "rnaseq",
    "software",
    "variantannotation"
  ],
  "_stars": 1,
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 477,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 391,
    "source": "https://www.bioconductor.org/packages/stats/bioc/OutSplice"
  },
  "_devurl": "https://github.com/guolabucsd/outsplice",
  "_searchresults": 13,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/OutSplice.html",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/guolabucsd/outsplice",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "outspliceAnalysis",
    "outspliceTCGA",
    "plotJunctionData"
  ],
  "_help": [
    {
      "page": "OutSplice",
      "title": "OutSplice package overview",
      "topics": [
        "OutSplice"
      ]
    },
    {
      "page": "outspliceAnalysis",
      "title": "Alternative Splicing Analyses",
      "topics": [
        "outspliceAnalysis"
      ]
    },
    {
      "page": "outspliceTCGA",
      "title": "Alternative Splicing Analysis for TCGA Data",
      "topics": [
        "outspliceTCGA"
      ]
    },
    {
      "page": "plotJunctionData",
      "title": "Create Plots of Junction Expression",
      "topics": [
        "plotJunctionData"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/OutSplice/raw/HEAD/README.md",
  "_rundeps": [
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "cachem",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "fastmap",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "glue",
    "httr",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lambda.r",
    "lifecycle",
    "memoise",
    "mime",
    "openssl",
    "org.Hs.eg.db",
    "pkgconfig",
    "png",
    "R6",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "sys",
    "TxDb.Hsapiens.UCSC.hg19.knownGene",
    "TxDb.Hsapiens.UCSC.hg38.knownGene",
    "vctrs",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "OutSplice.Rmd",
      "filename": "OutSplice.html",
      "title": "OutSplice",
      "author": "Joseph Bendik, Sandhya Kalavacherla, Michael Considine, Bahman Afsari, Michael F. Ochs, Joseph Califano, Daria A. Gaykalova, Elana Fertig, Theresa Guo",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Functionality",
        "Minimum required packages",
        "Installation from Bioconductor",
        "Inputs",
        "outspliceAnalysis/outspliceTCGA",
        "Phenotype matrix",
        "plotJunctionData",
        "Methodology",
        "Junction RPM normalization",
        "OGSA initial filtering",
        "OGSA outlier analysis",
        "Genomic references",
        "Junction expression normalization",
        "Filter by expression via offsets",
        "Splice Burden Calculation",
        "Junction Plotting",
        "Outputs",
        "outSpliceAnalysis/outSpliceTCGA",
        "References",
        "Session Info"
      ],
      "created": "2023-01-05 23:59:29",
      "modified": "2025-02-04 20:57:18",
      "commits": 18
    }
  ],
  "_score": 4.113943352306837,
  "_indexed": true,
  "_nocasepkg": "outsplice",
  "_universes": [
    "bioc",
    "theresaguo",
    "guolabucsd"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.13.0",
      "date": "2026-10-17T09:34:38.000Z",
      "distro": "resolute",
      "commit": "60d4ae860a4acd09106f01d4df4cc4a2da7459c0",
      "fileid": "https://r2.ropensci.org/4d307e4dcf702dff29f0492da1933e4b2623583e87b3d187ba6b2e0ad23f1011",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39020925716"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.13.0",
      "date": "2026-10-17T09:33:26.000Z",
      "distro": "resolute",
      "commit": "60d4ae860a4acd09106f01d4df4cc4a2da7459c0",
      "fileid": "https://r2.ropensci.org/b36ea72c38a39816dd409a3910ab7de1ea17ab138d0cb44e74756023d70e8686",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39020925716"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.13.0",
      "date": "2026-10-17T09:31:28.000Z",
      "commit": "60d4ae860a4acd09106f01d4df4cc4a2da7459c0",
      "fileid": "https://r2.ropensci.org/9fb2f145d5d12e2b3812a610a87f2495a3deaa637e6043e20dc19c432de81a78",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39020925716"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.13.0",
      "date": "2026-10-17T09:30:58.000Z",
      "commit": "60d4ae860a4acd09106f01d4df4cc4a2da7459c0",
      "fileid": "https://r2.ropensci.org/941eccecfd5be845ccb01038fba01cd0c32a8cb9ef14ef97b6e1a04fa46ebefc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39020925716"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.13.0",
      "date": "2026-10-17T09:32:01.000Z",
      "commit": "60d4ae860a4acd09106f01d4df4cc4a2da7459c0",
      "fileid": "https://r2.ropensci.org/7c13f2df6bf676ba912c0f03fad9a4e3ef3cc4cbcae951fd150a86dc60451589",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39020925716"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.13.0",
      "date": "2026-10-17T09:31:05.000Z",
      "commit": "60d4ae860a4acd09106f01d4df4cc4a2da7459c0",
      "fileid": "https://r2.ropensci.org/d54312f2c3b0212ed1e56ecf95b257ca67c83688ed2622790e0f709eb100cf06",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39020925716"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.13.0",
      "date": "2026-10-17T09:31:10.000Z",
      "commit": "60d4ae860a4acd09106f01d4df4cc4a2da7459c0",
      "fileid": "https://r2.ropensci.org/62b0ceaa8a35ce2b0236e95101ca2480728fee5d74bcdfe8e0387bcdd601e567",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39020925716"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.13.0",
      "date": "2026-10-17T09:30:49.000Z",
      "commit": "60d4ae860a4acd09106f01d4df4cc4a2da7459c0",
      "fileid": "https://r2.ropensci.org/8752fd9829d055932f201ff43a85f631eac2ecc58efaf450c0bb1a6606507a24",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39020925716"
    }
  ]
}