{
  "_id": "6ae845b82e87f76f20ace3c3",
  "Package": "SICtools",
  "Type": "Package",
  "Title": "Find SNV/Indel differences between two bam files with near\nrelationship",
  "Version": "1.43.1",
  "Date": "2014-12-11",
  "Author": "Xiaobin Xing, Wu Wei",
  "Maintainer": "Xiaobin Xing <xiaobinxing0316@gmail.com>",
  "Description": "This package is to find SNV/Indel differences between two\nbam files with near relationship in a way of pairwise\ncomparison thourgh each base position across the genome region\nof interest. The difference is inferred by fisher test and\neuclidean distance, the input of which is the base count\n(A,T,G,C) in a given position and read counts for indels that\nspan no less than 2bp on both sides of indel region.",
  "License": "GPL (>=2)",
  "LazyLoad": "Yes",
  "biocViews": "Alignment, Sequencing, Coverage, SequenceMatching,\nQualityControl, DataImport, Software, SNP, VariantDetection",
  "VignetteBuilder": "knitr",
  "Packaged": {
    "Date": "2026-10-31 12:26:41 UTC",
    "User": "root"
  },
  "Config/Bioconductor/UnsupportedPlatforms": "windows",
  "Config/pak/sysreqs": "libbz2-dev libicu-dev liblzma-dev xz-utils\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-29 18:37:11 UTC",
  "RemoteUrl": "https://github.com/bioc/SICtools",
  "RemoteRef": "HEAD",
  "RemoteSha": "344a04ae6c54136414ee064dd5c347429b07ca24",
  "NeedsCompilation": "yes",
  "_user": "bioc",
  "_type": "src",
  "_file": "SICtools_1.43.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/645e3c27330a8f1ff24f3ec3db508999f42324c232a703fa2de980486b42a2db",
  "_filesize": 1522414,
  "_sha256": "645e3c27330a8f1ff24f3ec3db508999f42324c232a703fa2de980486b42a2db",
  "_expires": "2027-02-08T13:42:20.000Z",
  "_created": "2026-10-31T12:26:41.000Z",
  "_published": "2026-11-02T08:11:36.065Z",
  "_upstream": "https://github.com/bioc/SICtools",
  "_status": "success",
  "_maintainer": {
    "name": "Xiaobin Xing",
    "email": "xiaobinxing0316@gmail.com"
  },
  "_jobs": [
    {
      "job": 125159185385,
      "time": 163,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13124673488"
    },
    {
      "job": 125159185605,
      "time": 185,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "13124439486"
    },
    {
      "job": 125159185547,
      "time": 302,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "13125710314"
    },
    {
      "job": 125159185486,
      "time": 173,
      "config": "linux-release-arm64",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13125281487"
    },
    {
      "job": 125159185539,
      "time": 292,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13125915206"
    },
    {
      "job": 125159185527,
      "time": 157,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "13125227474"
    },
    {
      "job": 125159185522,
      "time": 290,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "13125810440"
    },
    {
      "job": 125159185580,
      "time": 183,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13125312890"
    },
    {
      "job": 125159185524,
      "time": 466,
      "config": "macos-release-x86_64",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13125214016"
    },
    {
      "job": 125159186615,
      "time": 249,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "13042596703"
    },
    {
      "job": 125159185448,
      "time": 104,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 125159185697,
      "time": 174,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 125159185552,
      "time": 97,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 125159185619,
      "time": 66,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 125159185771,
      "time": 156,
      "config": "windows-release-arm64",
      "r": "4.6.2",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 125159185497,
      "time": 74,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "FAIL",
      "artifact": ""
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 2,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41200855236",
  "_commit": {
    "id": "344a04ae6c54136414ee064dd5c347429b07ca24",
    "author": "A Wokaty <awokaty@users.noreply.github.com>",
    "committer": "A Wokaty <awokaty@users.noreply.github.com>",
    "message": "Bump version\n",
    "time": 1780079831
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "Rsamtools",
      "version": ">= 1.18.1",
      "role": "Depends"
    },
    {
      "package": "doParallel",
      "version": ">= 1.0.8",
      "role": "Depends"
    },
    {
      "package": "Biostrings",
      "version": ">= 2.32.1",
      "role": "Depends"
    },
    {
      "package": "stringr",
      "version": ">= 0.6.2",
      "role": "Depends"
    },
    {
      "package": "matrixStats",
      "version": ">= 0.10.0",
      "role": "Depends"
    },
    {
      "package": "plyr",
      "version": ">= 1.8.3",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "version": ">= 1.22.4",
      "role": "Depends"
    },
    {
      "package": "IRanges",
      "version": ">= 2.4.8",
      "role": "Depends"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-22",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.43.1",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.42.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "alignment",
    "sequencing",
    "coverage",
    "sequencematching",
    "qualitycontrol",
    "dataimport",
    "software",
    "snp",
    "variantdetection"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 481,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 551,
    "source": "https://www.bioconductor.org/packages/stats/bioc/SICtools"
  },
  "_searchresults": 5,
  "_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/SICtools.html"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "indelDiff",
    "snpDiff"
  ],
  "_help": [
    {
      "page": "SICtools-package",
      "title": "tools for SNV/Indel Comparison between two bam files with near relationship",
      "topics": [
        "SICtools-package",
        "SICtools"
      ]
    },
    {
      "page": "indelDiff",
      "title": "main function to call indel difference between the bam files",
      "topics": [
        "indelDiff"
      ]
    },
    {
      "page": "snpDiff",
      "title": "main function to test point differences between the two bam files",
      "topics": [
        "snpDiff"
      ]
    }
  ],
  "_rundeps": [
    "BH",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "doParallel",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "glue",
    "IRanges",
    "iterators",
    "lambda.r",
    "lifecycle",
    "magrittr",
    "matrixStats",
    "plyr",
    "Rcpp",
    "Rhtslib",
    "rlang",
    "Rsamtools",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "stringi",
    "stringr",
    "vctrs",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "SICtools.Rmd",
      "filename": "SICtools.html",
      "title": "Using the SICtools Package",
      "author": "Xiaobin Xing",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction to SICtools",
        "Getting started with SICtools",
        "Function snpDiff()",
        "Input",
        "Output",
        "Example",
        "Function indelDiff()",
        "Input and Output",
        "Conclusion",
        "Session Info"
      ],
      "created": "2015-10-06 17:15:15",
      "modified": "2015-10-06 17:15:15",
      "commits": 1
    }
  ],
  "_score": 3.4771212547196626,
  "_indexed": true,
  "_nocasepkg": "sictools",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.43.1",
      "date": "2026-11-02T07:58:33.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "344a04ae6c54136414ee064dd5c347429b07ca24",
      "fileid": "https://r2.ropensci.org/e287e882d5beb210b92f5d9764eb0346a770c1916e7718d027a60de8848da183",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41200855236"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.43.1",
      "date": "2026-11-02T08:01:29.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "344a04ae6c54136414ee064dd5c347429b07ca24",
      "fileid": "https://r2.ropensci.org/843c1ea0a7a416c8656476bdfb75a1e34404d77e7b403bc8def3fc05886b1e86",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41200855236"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.43.1",
      "date": "2026-11-02T07:58:21.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "344a04ae6c54136414ee064dd5c347429b07ca24",
      "fileid": "https://r2.ropensci.org/88a2ab09b56dd536bb531308ca5187fcad6040f35c3b13c5b60b470c41010228",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41200855236"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.43.1",
      "date": "2026-11-02T08:01:11.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "344a04ae6c54136414ee064dd5c347429b07ca24",
      "fileid": "https://r2.ropensci.org/a8af5835649cdb90f0969635dde539c838655859d90dda003a7da5bcc42d9d60",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41200855236"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.43.1",
      "date": "2026-11-02T08:06:41.000Z",
      "arch": "aarch64",
      "commit": "344a04ae6c54136414ee064dd5c347429b07ca24",
      "fileid": "https://r2.ropensci.org/d5c102371646216f19ba5e0b77bbc3dfef76ede1342e2ef7eff8f8986bb5d069",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41200855236"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.43.1",
      "date": "2026-11-02T08:05:03.000Z",
      "arch": "x86_64",
      "commit": "344a04ae6c54136414ee064dd5c347429b07ca24",
      "fileid": "https://r2.ropensci.org/b3ba752366a90c540184bc5f30fc3ba2b5b5f749c56e3c45edff6f573372c79f",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41200855236"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.43.1",
      "date": "2026-11-02T08:06:44.000Z",
      "arch": "aarch64",
      "commit": "344a04ae6c54136414ee064dd5c347429b07ca24",
      "fileid": "https://r2.ropensci.org/d1b3b7bce751078057036e3e2f4c800f891f0362e173eb9c1b8c4b730c24f19e",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41200855236"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.43.1",
      "date": "2026-11-02T08:07:12.000Z",
      "arch": "x86_64",
      "commit": "344a04ae6c54136414ee064dd5c347429b07ca24",
      "fileid": "https://r2.ropensci.org/34ff05395178c8af3ad0b60f064b34b77e004faabefda49d5e4524c30c8ce942",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41200855236"
    }
  ]
}