{
  "_id": "6ac74bb6de46216d5edce074",
  "Package": "SICtools",
  "Type": "Package",
  "Title": "Find SNV/Indel differences between two bam files with near\nrelationship",
  "Version": "1.42.0",
  "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": "2026-10-06 13:48:20 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "libbz2-dev libicu-dev liblzma-dev xz-utils\nzlib1g-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:42:01 UTC",
  "RemoteUrl": "https://github.com/bioc/SICtools",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "f10f487004c07fae7c3f082c5003e9410e5cb5d6",
  "NeedsCompilation": "yes",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "SICtools_1.42.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/d5ef24657c26fc5d50410dcca6a3c309cb44962943fd7ba4c4d9adb01d8f6aed",
  "_filesize": 1522441,
  "_sha256": "d5ef24657c26fc5d50410dcca6a3c309cb44962943fd7ba4c4d9adb01d8f6aed",
  "_expires": "2027-01-14T13:55:43.000Z",
  "_created": "2026-10-06T13:48:20.000Z",
  "_published": "2026-10-08T07:52:22.525Z",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37473215255",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 1,
    "warning": 2,
    "note": 12
  },
  "_upstream": "https://github.com/bioc/SICtools",
  "_commit": {
    "id": "f10f487004c07fae7c3f082c5003e9410e5cb5d6",
    "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": 1777380121
  },
  "_maintainer": {
    "name": "Xiaobin Xing",
    "email": "xiaobinxing0316@gmail.com"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 113205611187,
      "time": 134,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11535941166"
    },
    {
      "job": 113205611161,
      "time": 186,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11535398346"
    },
    {
      "job": 113205611146,
      "time": 254,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11535049432"
    },
    {
      "job": 113205611210,
      "time": 202,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11535871645"
    },
    {
      "job": 113205611149,
      "time": 328,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11535966641"
    },
    {
      "job": 113205611177,
      "time": 136,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11535662154"
    },
    {
      "job": 113205611358,
      "time": 288,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11536031246"
    },
    {
      "job": 113205611241,
      "time": 153,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11535482614"
    },
    {
      "job": 113205611246,
      "time": 372,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11535836310"
    },
    {
      "job": 113205612153,
      "time": 247,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11417693133"
    },
    {
      "job": 113205611083,
      "time": 122,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 113205611184,
      "time": 174,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 113205611224,
      "time": 74,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 113205611132,
      "time": 63,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 113205611125,
      "time": 191,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 113205611176,
      "time": 62,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "FAIL",
      "artifact": ""
    }
  ],
  "_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": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_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": 473,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 496,
    "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": 3.3010299956639813,
  "_indexed": false,
  "_nocasepkg": "sictools",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/SICtools",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.42.0",
      "date": "2026-10-08T07:47:22.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "f10f487004c07fae7c3f082c5003e9410e5cb5d6",
      "fileid": "https://r2.ropensci.org/78568cbc632365536969877a0e62ac33277daf7a417ee2bc590a20d658d681ea",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37473215255"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.42.0",
      "date": "2026-10-08T07:48:29.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "f10f487004c07fae7c3f082c5003e9410e5cb5d6",
      "fileid": "https://r2.ropensci.org/3231db84e78d6557b445f95eb0937c7fcd2a4586e41660eafadf8749c4c70c1b",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37473215255"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.42.0",
      "date": "2026-10-08T07:47:36.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "f10f487004c07fae7c3f082c5003e9410e5cb5d6",
      "fileid": "https://r2.ropensci.org/3e144d69d3306539226289c7d7d0d3ce6d5d1c998def246a106af3f1dd439d52",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37473215255"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.42.0",
      "date": "2026-10-08T07:49:25.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "f10f487004c07fae7c3f082c5003e9410e5cb5d6",
      "fileid": "https://r2.ropensci.org/65f1522f28fae463f71f43fd0b80dc479aa8f8df7de6d3ea717bb7cad12157a3",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37473215255"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.42.0",
      "date": "2026-10-08T07:46:47.000Z",
      "arch": "aarch64",
      "commit": "f10f487004c07fae7c3f082c5003e9410e5cb5d6",
      "fileid": "https://r2.ropensci.org/3bf8a5820eb01906c7d647cef2315682b3e93c5c3a92e52c8d1531a4890c8bf3",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37473215255"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.42.0",
      "date": "2026-10-08T07:48:12.000Z",
      "arch": "x86_64",
      "commit": "f10f487004c07fae7c3f082c5003e9410e5cb5d6",
      "fileid": "https://r2.ropensci.org/317eb020c8d0dd4d212c78b7ebc2ed789f6ab60c74017b400f33c008ecf93a29",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37473215255"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.42.0",
      "date": "2026-10-08T07:46:53.000Z",
      "arch": "aarch64",
      "commit": "f10f487004c07fae7c3f082c5003e9410e5cb5d6",
      "fileid": "https://r2.ropensci.org/7914a5b4020e87b6170806b3cfae1f69743182e598c02c0f7324528cff8b6642",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37473215255"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.42.0",
      "date": "2026-10-08T07:48:46.000Z",
      "arch": "x86_64",
      "commit": "f10f487004c07fae7c3f082c5003e9410e5cb5d6",
      "fileid": "https://r2.ropensci.org/a7ee1ae27378cd746505e038e0d9665a31c378538ae560f7c3420b4e6f14f5a9",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37473215255"
    }
  ]
}