{
  "_id": "6a391780b6829d88cf70bae0",
  "Package": "REDseq",
  "Type": "Package",
  "Title": "Analysis of high-throughput sequencing data processed by\nrestriction enzyme digestion",
  "Version": "1.59.0",
  "Date": "2021-05-02",
  "Author": "Lihua Julie Zhu, Junhui Li and Thomas Fazzio",
  "Maintainer": "Lihua Julie Zhu <julie.zhu@umassmed.edu>",
  "biocViews": "Sequencing, SequenceMatching, Preprocessing",
  "Description": "The package includes functions to build restriction enzyme\ncut site (RECS) map, distribute mapped sequences on the map\nwith five different approaches, find enriched/depleted RECSs\nfor a sample, and identify differentially enriched/depleted\nRECSs between samples.",
  "License": "GPL (>=2)",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:35:28 UTC",
  "RemoteUrl": "https://github.com/bioc/REDseq",
  "RemoteRef": "HEAD",
  "RemoteSha": "c566c72a8012c0487d553e691dae65aec1721e6a",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-22 10:58:18 UTC",
    "User": "root"
  },
  "MD5sum": "21b6aff329e012d15940a989a2445984",
  "_user": "bioc",
  "_type": "src",
  "_file": "REDseq_1.59.0.tar.gz",
  "_fileid": "8e34293828105eb8b7e1d939b4962d4134869ff9ed285bd5acaa5d15b9e068cf",
  "_filesize": 280800,
  "_sha256": "8e34293828105eb8b7e1d939b4962d4134869ff9ed285bd5acaa5d15b9e068cf",
  "_created": "2026-06-22T10:58:18.000Z",
  "_published": "2026-06-22T11:07:44.059Z",
  "_jobs": [
    {
      "job": 82697010578,
      "time": 385,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7790446451"
    },
    {
      "job": 82697010601,
      "time": 494,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7790485858"
    },
    {
      "job": 82697010607,
      "time": 479,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7790480891"
    },
    {
      "job": 82697010621,
      "time": 276,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7790407864"
    },
    {
      "job": 82697010589,
      "time": 352,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7790434921"
    },
    {
      "job": 82695972044,
      "time": 354,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7790304605"
    },
    {
      "job": 82697010591,
      "time": 171,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7790367992"
    },
    {
      "job": 82697010617,
      "time": 431,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7790463509"
    },
    {
      "job": 82697010592,
      "time": 378,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7790443770"
    },
    {
      "job": 82697010599,
      "time": 363,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7790439096"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 3,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/27947511415",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/REDseq",
  "_commit": {
    "id": "c566c72a8012c0487d553e691dae65aec1721e6a",
    "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": 1777379728
  },
  "_maintainer": {
    "name": "Lihua Julie Zhu",
    "email": "julie.zhu@umassmed.edu",
    "login": "lihuajuliezhu",
    "description": "",
    "uuid": 30300372
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "BiocGenerics",
      "role": "Depends"
    },
    {
      "package": "BSgenome.Celegans.UCSC.ce2",
      "role": "Depends"
    },
    {
      "package": "multtest",
      "role": "Depends"
    },
    {
      "package": "Biostrings",
      "role": "Depends"
    },
    {
      "package": "BSgenome",
      "role": "Depends"
    },
    {
      "package": "ChIPpeakAnno",
      "role": "Depends"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "version": ">= 1.13.5",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.59.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.58.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "sequencing",
    "sequencematching",
    "preprocessing"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 441,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 1,
  "_searchresults": 15,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/REDseq.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "assignSeq2REsite",
    "binom.test.REDseq",
    "buildREmap",
    "compareREDseq",
    "distanceHistSeq2RE",
    "plotCutDistribution",
    "summarizeByRE",
    "summarizeBySeq"
  ],
  "_datasets": [
    {
      "name": "example.assignedREDseq",
      "title": "an example assigned REDseq dataset",
      "object": "example.assignedREDseq",
      "file": "example.assignedREDseq.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "example.map",
      "title": "an example REmap dataset",
      "object": "example.map",
      "file": "example.map.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "example.REDseq",
      "title": "an example sequencing dataset from a restoration enzyme digestion (RED) experiment",
      "object": "example.REDseq",
      "file": "example.REDseq.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "REDseq-package",
      "title": "REDseq",
      "topics": [
        "REDseq-package",
        "REDseq"
      ]
    },
    {
      "page": "assignSeq2REsite",
      "title": "Assign mapped sequence tags to corresponding restriction enzyme (RE) cut sites",
      "topics": [
        "assignSeq2REsite"
      ]
    },
    {
      "page": "binom.test.REDseq",
      "title": "Binomial test for REDseq dataset",
      "topics": [
        "binom.test.REDseq"
      ]
    },
    {
      "page": "buildREmap",
      "title": "Build a genome wide cut site map for a Restriction Enzyme (RE)",
      "topics": [
        "buildREmap"
      ]
    },
    {
      "page": "compareREDseq",
      "title": "Compare two RED Sequencing Dataset",
      "topics": [
        "compareREDseq"
      ]
    },
    {
      "page": "distanceHistSeq2RE",
      "title": "Plot the distance distribution from sequence to the associated RE sites",
      "topics": [
        "distanceHistSeq2RE"
      ]
    },
    {
      "page": "example.assignedREDseq",
      "title": "an example assigned REDseq dataset",
      "topics": [
        "example.assignedREDseq"
      ]
    },
    {
      "page": "example.map",
      "title": "an example REmap dataset",
      "topics": [
        "example.map"
      ]
    },
    {
      "page": "example.REDseq",
      "title": "an example sequencing dataset from a restoration enzyme digestion (RED) experiment",
      "topics": [
        "example.REDseq"
      ]
    },
    {
      "page": "plotCutDistribution",
      "title": "plot cut frequencies of RE sites along a given chromosome",
      "topics": [
        "plotCutDistribution"
      ]
    },
    {
      "page": "summarizeByRE",
      "title": "Output count/weight summary by restriction enzyme cut site ID (REid)",
      "topics": [
        "summarizeByRE"
      ]
    },
    {
      "page": "summarizeBySeq",
      "title": "Output count/weight summary by sequences",
      "topics": [
        "summarizeBySeq"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationFilter",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "biomaRt",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "BSgenome.Celegans.UCSC.ce2",
    "cachem",
    "ChIPpeakAnno",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dplyr",
    "ensembldb",
    "farver",
    "fastmap",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "graph",
    "gtable",
    "hms",
    "httr",
    "httr2",
    "InteractionSet",
    "IRanges",
    "isoband",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "lambda.r",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "multtest",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "ProtGenerics",
    "purrr",
    "pwalign",
    "R6",
    "rappdirs",
    "RBGL",
    "RColorBrewer",
    "Rcpp",
    "RcppThread",
    "RCurl",
    "regioneR",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "UCSC.utils",
    "universalmotif",
    "utf8",
    "vctrs",
    "VennDiagram",
    "viridisLite",
    "withr",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "REDseq.Rnw",
      "filename": "REDseq.pdf",
      "title": "REDseq Vignette",
      "engine": "utils::Sweave",
      "headings": [
        "Introduction",
        "Examples of using REDseq",
        "References",
        "Session Info"
      ],
      "created": "2013-10-21 15:43:23",
      "modified": "2021-03-10 20:42:41",
      "commits": 3
    }
  ],
  "_score": 3.4771212547196626,
  "_indexed": true,
  "_nocasepkg": "redseq",
  "_universes": [
    "bioc",
    "lihuajuliezhu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.59.0",
      "date": "2026-06-22T11:02:56.000Z",
      "distro": "noble",
      "commit": "c566c72a8012c0487d553e691dae65aec1721e6a",
      "fileid": "a53afe43b153168e8de91e47e0b61042059772b602a2ad6ac2c75748b5abc9b6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27947511415"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.59.0",
      "date": "2026-06-22T11:02:45.000Z",
      "distro": "noble",
      "commit": "c566c72a8012c0487d553e691dae65aec1721e6a",
      "fileid": "c1f123f0ffc60280a0a63efb4c40fca29c62e1ca62045e9777a768480d310cc6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27947511415"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.59.0",
      "date": "2026-06-22T11:00:56.000Z",
      "commit": "c566c72a8012c0487d553e691dae65aec1721e6a",
      "fileid": "866a064906e3d7f4117ea61e64785ec3ea6855d019d8a70e23880b00621a6a33",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27947511415"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.59.0",
      "date": "2026-06-22T11:01:19.000Z",
      "commit": "c566c72a8012c0487d553e691dae65aec1721e6a",
      "fileid": "752759f54b5d01f7cd3dac5d512b04b1168e91762ade8dd62da84e7648fd1e64",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27947511415"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.59.0",
      "date": "2026-06-22T11:01:52.000Z",
      "commit": "c566c72a8012c0487d553e691dae65aec1721e6a",
      "fileid": "de791cee7bcc06982db95b9f037657ba7b38bd856999f74d1a94241a756780b5",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27947511415"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.59.0",
      "date": "2026-06-22T11:01:42.000Z",
      "commit": "c566c72a8012c0487d553e691dae65aec1721e6a",
      "fileid": "9023c0e7f899cebbdabd31c9534fbef204ebf050fcecfc36303bf2243d95dcfd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27947511415"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.59.0",
      "date": "2026-06-22T11:00:56.000Z",
      "commit": "c566c72a8012c0487d553e691dae65aec1721e6a",
      "fileid": "d3c65dbaaa9dd0c1ad5f1b6c23248931c732ac279dab9b16264da12878d7a5bc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27947511415"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.59.0",
      "date": "2026-06-22T11:00:53.000Z",
      "commit": "c566c72a8012c0487d553e691dae65aec1721e6a",
      "fileid": "046cc5a26fd8d856f0a6a92f0a0490e8b1aa0b2b0e22c996db39e9875890e60f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27947511415"
    }
  ]
}