{
  "_id": "6a49413918cdde069385df31",
  "Package": "FilterFFPE",
  "Type": "Package",
  "Title": "FFPE Artificial Chimeric Read Filter for NGS data",
  "Version": "1.23.0",
  "Authors@R": "person(\"Lanying\", \"Wei\", email=\"lanying.wei@uni-muenster.de\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4281-8017\"))",
  "Description": "This package finds and filters artificial chimeric reads\nspecifically generated in next-generation sequencing (NGS)\nprocess of formalin-fixed paraffin-embedded (FFPE) tissues.\nThese artificial chimeric reads can lead to a large number of\nfalse positive structural variation (SV) calls. The required\ninput is an indexed BAM file of a FFPE sample.",
  "License": "LGPL-3",
  "Encoding": "UTF-8",
  "biocViews": "StructuralVariation, Sequencing, Alignment, QualityControl,\nPreprocessing",
  "Config/pak/sysreqs": "libbz2-dev liblzma-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:53:40 UTC",
  "RemoteUrl": "https://github.com/bioc/FilterFFPE",
  "RemoteRef": "HEAD",
  "RemoteSha": "b5ae7a79d9200b99e31febb0792b162c2fa8a0cd",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-04 07:46:21 UTC",
    "User": "root"
  },
  "Author": "Lanying Wei [aut, cre] (ORCID: <https://orcid.org/0000-0002-4281-8017>)",
  "Maintainer": "Lanying Wei <lanying.wei@uni-muenster.de>",
  "_user": "bioc",
  "_type": "src",
  "_file": "FilterFFPE_1.23.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/b67c0df64f815b25b8553f7b09926166e6ed9ba4147a98860cb1832308e32f9d",
  "_filesize": 1471025,
  "_sha256": "b67c0df64f815b25b8553f7b09926166e6ed9ba4147a98860cb1832308e32f9d",
  "_expires": "2026-10-12T17:22:00.000Z",
  "_created": "2026-07-04T07:46:21.000Z",
  "_published": "2026-07-04T17:22:01.744Z",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 8
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28699453024",
  "_status": "success",
  "_upstream": "https://github.com/bioc/FilterFFPE",
  "_commit": {
    "id": "b5ae7a79d9200b99e31febb0792b162c2fa8a0cd",
    "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": 1777380820
  },
  "_maintainer": {
    "name": "Lanying Wei",
    "email": "lanying.wei@uni-muenster.de",
    "login": "lanyingwei",
    "description": "",
    "uuid": 49517206,
    "orcid": "0000-0002-4281-8017"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85151783388,
      "time": 167,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8079762287"
    },
    {
      "job": 85151783353,
      "time": 252,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8079772109"
    },
    {
      "job": 85151783432,
      "time": 271,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8079774267"
    },
    {
      "job": 85151783357,
      "time": 156,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8080107636"
    },
    {
      "job": 85151783335,
      "time": 197,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8080106701"
    },
    {
      "job": 85151783183,
      "time": 271,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8079740681"
    },
    {
      "job": 85151783414,
      "time": 138,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8079758734"
    },
    {
      "job": 85151783502,
      "time": 202,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8079766128"
    },
    {
      "job": 85151783498,
      "time": 197,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8079765737"
    },
    {
      "job": 85151783536,
      "time": 204,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8079766426"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.23.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.22.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "structuralvariation",
    "sequencing",
    "alignment",
    "qualitycontrol",
    "preprocessing"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 1,
  "_searchresults": 1,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/FilterFFPE.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "FFPEReadFilter",
    "filterBamByReadNames",
    "findArtifactChimericReads"
  ],
  "_help": [
    {
      "page": "FilterFFPE-package",
      "title": "FFPE Artificial Chimeric Read Filter for NGS data",
      "topics": [
        "FilterFFPE-package",
        "FilterFFPE"
      ]
    },
    {
      "page": "FFPEReadFilter",
      "title": "Find and filter artifact chimeric reads in BAM file of FFPE sample",
      "topics": [
        "FFPEReadFilter"
      ]
    },
    {
      "page": "filterBamByReadNames",
      "title": "Filter reads from BAM file by read names",
      "topics": [
        "filterBamByReadNames"
      ]
    },
    {
      "page": "findArtifactChimericReads",
      "title": "Find artifact chimeric reads in BAM file of FFPE sample",
      "topics": [
        "findArtifactChimericReads"
      ]
    }
  ],
  "_rundeps": [
    "BH",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "codetools",
    "cpp11",
    "crayon",
    "doParallel",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "IRanges",
    "iterators",
    "lambda.r",
    "Rhtslib",
    "Rsamtools",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "FilterFFPE.Rnw",
      "filename": "FilterFFPE.pdf",
      "title": "An introduction to FilterFFPE",
      "engine": "utils::Sweave",
      "headings": [
        "1 Introduction",
        "2 Input",
        "3 Artifact Chimeric Read Filtration",
        "A Session info"
      ],
      "created": "2020-09-18 14:19:06",
      "modified": "2020-11-11 20:50:38",
      "commits": 2
    }
  ],
  "_score": 3.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "filterffpe",
  "_universes": [
    "bioc",
    "lanyingwei"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-07-04T07:49:16.000Z",
      "distro": "resolute",
      "commit": "b5ae7a79d9200b99e31febb0792b162c2fa8a0cd",
      "fileid": "https://r2.ropensci.org/56deb7312bf317f60d33c59da95ce9a98eb9a0732ce75670fd50e9c7d720f124",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699453024"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-07-04T07:49:25.000Z",
      "distro": "resolute",
      "commit": "b5ae7a79d9200b99e31febb0792b162c2fa8a0cd",
      "fileid": "https://r2.ropensci.org/901449c35b33fb652a34466b7c8cb26ac47b905e77354125b187f06c9977101d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699453024"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-07-04T08:37:32.000Z",
      "commit": "b5ae7a79d9200b99e31febb0792b162c2fa8a0cd",
      "fileid": "https://r2.ropensci.org/650106442f77639b3c0d07025c0fd5f68763c81d8081bcb6190853ada2656f04",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699453024"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-07-04T08:36:50.000Z",
      "commit": "b5ae7a79d9200b99e31febb0792b162c2fa8a0cd",
      "fileid": "https://r2.ropensci.org/73ebfc0b0634ecc42e07ec21cb46765d574d7250383aaeb885a73f4fef382bd0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699453024"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.23.0",
      "date": "2026-07-04T07:49:02.000Z",
      "commit": "b5ae7a79d9200b99e31febb0792b162c2fa8a0cd",
      "fileid": "https://r2.ropensci.org/cd0066ebc973f3aadc0579898b51b493257384288f1ac30be45c30dfa9e5b856",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699453024"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-07-04T07:48:22.000Z",
      "commit": "b5ae7a79d9200b99e31febb0792b162c2fa8a0cd",
      "fileid": "https://r2.ropensci.org/b257227064abb5d7ce2c7671a2263242ef98bad484659b4a1ade24a8c3958c59",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699453024"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-07-04T07:47:52.000Z",
      "commit": "b5ae7a79d9200b99e31febb0792b162c2fa8a0cd",
      "fileid": "https://r2.ropensci.org/ce3f53e10b44bb1fccf172b6054eb1bf81299e8829fc613a79b7344d3fe4483a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699453024"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-07-04T07:47:56.000Z",
      "commit": "b5ae7a79d9200b99e31febb0792b162c2fa8a0cd",
      "fileid": "https://r2.ropensci.org/f8274e32d33f54d6951bb4aeb1725ca6de795dabd6350055ff949cea0e26cdcd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699453024"
    }
  ]
}