{
  "_id": "6af1cb3594cdbf48db2b1eee",
  "Package": "Ularcirc",
  "Type": "Package",
  "Title": "Shiny app for canonical and back splicing analysis (i.e.\ncircular and mRNA analysis)",
  "Version": "1.30.0",
  "Authors@R": "person (\"David\", \"Humphreys\", email=\"d.humphreys@victorchang.edu.au\", \nrole = c(\"aut\",\"cre\"))",
  "Description": "Ularcirc reads in STAR aligned splice junction files and\nprovides visualisation and analysis tools for splicing\nanalysis. Users can assess backsplice junctions and forward\ncanonical junctions.",
  "biocViews": "DataRepresentation,Visualization, Genetics, Sequencing,\nAnnotation, Coverage, AlternativeSplicing, DifferentialSplicing",
  "License": "file LICENSE",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev xz-utils\nzlib1g-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:48:08 UTC",
  "RemoteUrl": "https://github.com/bioc/Ularcirc",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "632b8f304cd937f3212d9153c32ea68d9144b5c6",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-09 13:12:11 UTC",
    "User": "root"
  },
  "Author": "David Humphreys [aut, cre]",
  "Maintainer": "David Humphreys <d.humphreys@victorchang.edu.au>",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "Ularcirc_1.30.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/fdefc2f0e893f8e46feffb6d9bf9d5896aaedc93093569854ffff2942e04c4d5",
  "_filesize": 5382095,
  "_sha256": "fdefc2f0e893f8e46feffb6d9bf9d5896aaedc93093569854ffff2942e04c4d5",
  "_expires": "2027-02-17T13:31:31.000Z",
  "_created": "2026-11-09T13:12:11.000Z",
  "_published": "2026-11-09T13:31:32.958Z",
  "_upstream": "https://github.com/bioc/Ularcirc",
  "_status": "success",
  "_maintainer": {
    "name": "David Humphreys",
    "email": "d.humphreys@victorchang.edu.au",
    "login": "davhum",
    "description": "RNA biologist/bioinformatician",
    "uuid": 4456671
  },
  "_jobs": [
    {
      "job": 129181135291,
      "time": 310,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13678210948"
    },
    {
      "job": 129181135235,
      "time": 364,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "13678136161"
    },
    {
      "job": 129181135334,
      "time": 370,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "WARNING",
      "artifact": "13677377176"
    },
    {
      "job": 129181135634,
      "time": 230,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "13678791539"
    },
    {
      "job": 129181135129,
      "time": 209,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "WARNING",
      "artifact": "13677592345"
    },
    {
      "job": 129178216745,
      "time": 355,
      "config": "source",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13677256154"
    },
    {
      "job": 129181135112,
      "time": 291,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13677154799"
    },
    {
      "job": 129181135728,
      "time": 240,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "13677203686"
    },
    {
      "job": 129181135236,
      "time": 270,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "13676429401"
    },
    {
      "job": 129181135411,
      "time": 238,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "WARNING",
      "artifact": "13677881073"
    }
  ],
  "_bioccheck": {
    "error": 3,
    "warning": 1,
    "note": 15
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42622540518",
  "_commit": {
    "id": "632b8f304cd937f3212d9153c32ea68d9144b5c6",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777380488
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4.0",
      "role": "Depends"
    },
    {
      "package": "AnnotationHub",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "BSgenome",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "version": ">= 1.9.4",
      "role": "Imports"
    },
    {
      "package": "DT",
      "role": "Imports"
    },
    {
      "package": "GenomicFeatures",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDbData",
      "role": "Imports"
    },
    {
      "package": "GenomicAlignments",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "gsubfn",
      "role": "Imports"
    },
    {
      "package": "moments",
      "role": "Imports"
    },
    {
      "package": "Organism.dplyr",
      "role": "Imports"
    },
    {
      "package": "plotgardener",
      "role": "Imports"
    },
    {
      "package": "R.utils",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "shinydashboard",
      "role": "Imports"
    },
    {
      "package": "shinyFiles",
      "role": "Imports"
    },
    {
      "package": "shinyjs",
      "role": "Imports"
    },
    {
      "package": "yaml",
      "role": "Imports"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg38",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "httpuv",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg38.knownGene",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.31.0",
      "bioc": "3.24",
      "repository": "bioc",
      "r": "4.6.0"
    },
    {
      "branch": "release",
      "version": "1.30.0",
      "bioc": "3.23",
      "repository": "bioc",
      "r": "4.6.0"
    }
  ],
  "_topics": [
    "datarepresentation",
    "visualization",
    "genetics",
    "sequencing",
    "annotation",
    "coverage",
    "alternativesplicing",
    "differentialsplicing"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 485,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 492,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Ularcirc"
  },
  "_mentions": 2,
  "_searchresults": 4,
  "_rbuild": "4.6.2",
  "_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/readme.html",
    "extra/readme.md",
    "extra/Ularcirc.html",
    "LICENSE"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "BSJ_details",
    "bsj_fastq_generate",
    "bsj_to_circRNA_sequence",
    "chimericStats",
    "circSequence",
    "Compatible_Annotation_DBs",
    "FilterChimericJuncs",
    "loadSTAR_chimeric",
    "miR_binding_site_Analysis",
    "plot_AllJunctions",
    "RAD_score",
    "SelectUniqueJunctions",
    "Ularcirc"
  ],
  "_help": [
    {
      "page": "BSJ_details",
      "title": "BSJ_details This function returns details of a BSJ string and returns a list of coordinates. Can accept two different formats, Ularcirc or generic.",
      "topics": [
        "BSJ_details"
      ]
    },
    {
      "page": "bsj_fastq_generate",
      "title": "bsj_fastq_generate",
      "topics": [
        "bsj_fastq_generate"
      ]
    },
    {
      "page": "bsj_to_circRNA_sequence",
      "title": "bsj_to_circRNA_sequence",
      "topics": [
        "bsj_to_circRNA_sequence"
      ]
    },
    {
      "page": "chimericFilters",
      "title": "chimericFilters",
      "topics": [
        "chimericFilters"
      ]
    },
    {
      "page": "chimericStats",
      "title": "chimericStats",
      "topics": [
        "chimericStats"
      ]
    },
    {
      "page": "circSequence",
      "title": "circSequence This function returns pre-defined full length circRNA sequences.",
      "topics": [
        "circSequence"
      ]
    },
    {
      "page": "Compatible_Annotation_DBs",
      "title": "Compatible_Annotation_DBs",
      "topics": [
        "Compatible_Annotation_DBs"
      ]
    },
    {
      "page": "FilterChimeric_Ularcirc",
      "title": "Wrapper function for Ularcirc shiny app which expects a list of objects to be returned",
      "topics": [
        "FilterChimeric_Ularcirc"
      ]
    },
    {
      "page": "FilterChimericJuncs",
      "title": "FilterChimericJuncs",
      "topics": [
        "FilterChimericJuncs"
      ]
    },
    {
      "page": "Junction_Sequence_from_Genome",
      "title": "Grab_BS_Junc_Sequence",
      "topics": [
        "Junction_Sequence_from_Genome"
      ]
    },
    {
      "page": "load_miRBase_fasta",
      "title": "load_miRBase_fasta This function extracts species specific mirbase sequences as a Biostrings RNAstringset.",
      "topics": [
        "load_miRBase_fasta"
      ]
    },
    {
      "page": "loadSTAR_chimeric",
      "title": "loadSTAR_chimeric",
      "topics": [
        "loadSTAR_chimeric"
      ]
    },
    {
      "page": "miR_binding_site_Analysis",
      "title": "miR_binding_site_Analysis This function analyses a genomic (RNA or DNA) sequence for matching miRNA seed sequences.",
      "topics": [
        "miR_binding_site_Analysis"
      ]
    },
    {
      "page": "plot_AllJunctions",
      "title": "plot_AllJunctions",
      "topics": [
        "plot_AllJunctions"
      ]
    },
    {
      "page": "RAD_score",
      "title": "RAD_score",
      "topics": [
        "RAD_score"
      ]
    },
    {
      "page": "SelectUniqueJunctions",
      "title": "SelectUniqueJunctions",
      "topics": [
        "SelectUniqueJunctions"
      ]
    },
    {
      "page": "sequence_from_exon_coords",
      "title": "sequence_from_exon_coords",
      "topics": [
        "sequence_from_exon_coords"
      ]
    },
    {
      "page": "Ularcirc",
      "title": "Ularcirc",
      "topics": [
        "Ularcirc"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/Ularcirc/raw/RELEASE_3_23/readme.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationFilter",
    "AnnotationHub",
    "askpass",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "biocmake",
    "BiocManager",
    "BiocParallel",
    "BiocVersion",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "bslib",
    "cachem",
    "cigarillo",
    "cli",
    "codetools",
    "commonmark",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "digest",
    "dir.expiry",
    "dplyr",
    "DT",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomeInfoDbData",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "ggplot2",
    "ggplotify",
    "ggrepel",
    "glue",
    "gridGraphics",
    "gsubfn",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "httr2",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "moments",
    "openssl",
    "Organism.dplyr",
    "otel",
    "pillar",
    "pkgconfig",
    "plotgardener",
    "plyranges",
    "png",
    "promises",
    "proto",
    "purrr",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "restfulr",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "Rhtslib",
    "rjson",
    "rlang",
    "rmarkdown",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shiny",
    "shinydashboard",
    "shinyFiles",
    "shinyjs",
    "snow",
    "sourcetools",
    "SparseArray",
    "strawr",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "UCSC.utils",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "xtable",
    "XVector",
    "yaml",
    "yulab.utils"
  ],
  "_vignettes": [
    {
      "source": "Ularcirc.Rmd",
      "filename": "Ularcirc.html",
      "title": "Ularcirc: A shiny application for canonical and back splicing analysis",
      "author": "David Humphreys, Nicolas Fossat, Patrick Tam, Joshua Ho",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Quickstart",
        "Preparing input data sets",
        "Splice junction files",
        "Annotation databases",
        "Workflow",
        "Step 1a: Loading annotation data",
        "Step 1b: Setting filters",
        "Genomic filters",
        "circRNA filters",
        "Step 1c: Loading new data sets",
        "Step 2a: Saving/loading a project and grouping samples",
        "Step 2b: Grouping samples",
        "Step 3a : Generating BSJ counts",
        "Step 3b : Visualising gene splicing patterns",
        "Exploring slicing patterns from any genomic region",
        "Step 5: Sequence analysis of splice/backsplice junctions",
        "Session Information-----------------------------------"
      ],
      "created": "2019-08-23 12:47:47",
      "modified": "2019-10-24 11:11:32",
      "commits": 2
    }
  ],
  "_score": 4,
  "_indexed": false,
  "_nocasepkg": "ularcirc",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/Ularcirc",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.30.0",
      "date": "2026-11-09T13:17:29.000Z",
      "distro": "resolute",
      "commit": "632b8f304cd937f3212d9153c32ea68d9144b5c6",
      "fileid": "https://r2.ropensci.org/119167186c31a24d3c2ff762b810fff98dc0dbe3a1aaa644f67e62480496316b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42622540518"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.30.0",
      "date": "2026-11-09T13:17:47.000Z",
      "distro": "resolute",
      "commit": "632b8f304cd937f3212d9153c32ea68d9144b5c6",
      "fileid": "https://r2.ropensci.org/6d65a2e24b95d347970bc19662fa763cf7821f87d4ad48034a4df3df5e5a9b6c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42622540518"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.30.0",
      "date": "2026-11-09T13:30:06.000Z",
      "commit": "632b8f304cd937f3212d9153c32ea68d9144b5c6",
      "fileid": "https://r2.ropensci.org/7490d839c47a5ba6480411e3903784a1845d227360a61e28243e33ce399f2c2d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42622540518"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.30.0",
      "date": "2026-11-09T13:20:10.000Z",
      "commit": "632b8f304cd937f3212d9153c32ea68d9144b5c6",
      "fileid": "https://r2.ropensci.org/6e062fcce27042f0701e5ab6fe0cc8dbf700b10b894012af280af2290fb5d1c0",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42622540518"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.30.0",
      "date": "2026-11-09T13:17:24.000Z",
      "commit": "632b8f304cd937f3212d9153c32ea68d9144b5c6",
      "fileid": "https://r2.ropensci.org/e8d4fd1b7b887a9aabcf413ee0697262a1404fa06f584480a1d8a1a82813f585",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42622540518"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.30.0",
      "date": "2026-11-09T13:15:09.000Z",
      "commit": "632b8f304cd937f3212d9153c32ea68d9144b5c6",
      "fileid": "https://r2.ropensci.org/8ff2a2802b6d6ea4f2e979af177d4b05d7268652db7f7951c3d1856429bb6ffb",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42622540518"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.30.0",
      "date": "2026-11-09T13:15:43.000Z",
      "commit": "632b8f304cd937f3212d9153c32ea68d9144b5c6",
      "fileid": "https://r2.ropensci.org/619172000db89f41d7f8611763616e6db78e50a2af2d86438e29123cf36e9794",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42622540518"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.30.0",
      "date": "2026-11-09T13:15:12.000Z",
      "commit": "632b8f304cd937f3212d9153c32ea68d9144b5c6",
      "fileid": "https://r2.ropensci.org/6ea0569dc55d903cc0a8b6c2e3e987c40dd60cfebbcd87c32dcef2fb35a3add5",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42622540518"
    }
  ]
}