{
  "_id": "6a1af6e91d7bb097a09f9ffb",
  "Package": "SeqSQC",
  "Title": "A bioconductor package for sample quality check with next\ngeneration sequencing data",
  "Version": "1.35.0",
  "Authors@R": "person(\"Qian\", \"Liu\", email = \"qliu7@buffalo.edu\", role = c(\"aut\", \"cre\"))",
  "Description": "The SeqSQC is designed to identify problematic samples in\nNGS data, including samples with gender mismatch,\ncontamination, cryptic relatedness, and population outlier.",
  "biocViews": "Experiment Data, Homo_sapiens_Data, Sequencing Data,\nProject1000genomes, Genome",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "URL": "https://github.com/Liubuntu/SeqSQC",
  "BugReports": "https://github.com/Liubuntu/SeqSQC/issues",
  "RoxygenNote": "7.3.1",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:46:47 UTC",
  "RemoteUrl": "https://github.com/bioc/SeqSQC",
  "RemoteRef": "HEAD",
  "RemoteSha": "d08f6591c9eb065e3d75ba9c6be3fafed18e5340",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:47:23 UTC",
    "User": "root"
  },
  "Author": "Qian Liu [aut, cre]",
  "Maintainer": "Qian Liu <qliu7@buffalo.edu>",
  "MD5sum": "a09a5f40ae4715a5fa36fb0030738a66",
  "_user": "bioc",
  "_type": "src",
  "_file": "SeqSQC_1.35.0.tar.gz",
  "_fileid": "263d9b6f527b455b993cf80a28a75f1c6d822d634208812c5782cfc45bf9da8e",
  "_filesize": 3525475,
  "_sha256": "263d9b6f527b455b993cf80a28a75f1c6d822d634208812c5782cfc45bf9da8e",
  "_created": "2026-05-30T09:47:23.000Z",
  "_published": "2026-05-30T14:40:41.817Z",
  "_jobs": [
    {
      "job": 78640647143,
      "time": 182,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307493585"
    },
    {
      "job": 78640647155,
      "time": 740,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307541174"
    },
    {
      "job": 78640647144,
      "time": 805,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307547462"
    },
    {
      "job": 78640647150,
      "time": 211,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7308940255"
    },
    {
      "job": 78640647151,
      "time": 247,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7308944518"
    },
    {
      "job": 78639923758,
      "time": 258,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307293443"
    },
    {
      "job": 78640647145,
      "time": 154,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307491364"
    },
    {
      "job": 78640647166,
      "time": 266,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307498861"
    },
    {
      "job": 78640647165,
      "time": 355,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7307508901"
    },
    {
      "job": 78640647162,
      "time": 223,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307495461"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 5,
    "note": 13
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676991840",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/SeqSQC",
  "_commit": {
    "id": "d08f6591c9eb065e3d75ba9c6be3fafed18e5340",
    "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": 1777380407
  },
  "_maintainer": {
    "name": "Qian Liu",
    "email": "qliu7@buffalo.edu",
    "login": "liubuntu",
    "twitter": "@QianLiu28878838",
    "description": "Assistant Professor in Department of Biostats & Bioinfo\nAlumni @Bioconductor Core Team",
    "uuid": 12683977
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4",
      "role": "Depends"
    },
    {
      "package": "ExperimentHub",
      "version": ">= 1.3.7",
      "role": "Depends"
    },
    {
      "package": "SNPRelate",
      "version": ">= 1.10.2",
      "role": "Depends"
    },
    {
      "package": "e1071",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "gdsfmt",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "GGally",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "plotly",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.35.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.34.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "experiment data",
    "homo_sapiens_data",
    "sequencing data",
    "project1000genomes",
    "genome"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "liubuntu",
      "count": 28,
      "uuid": 12683977
    },
    {
      "user": "nturaga",
      "count": 4,
      "uuid": 2746443
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "hubentu",
      "count": 2,
      "uuid": 9856666
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "link-ny",
      "count": 1,
      "uuid": 4392950
    },
    {
      "user": "qhu75",
      "count": 1,
      "uuid": 71154759
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 380,
    "source": "https://www.bioconductor.org/packages/stats/bioc/SeqSQC"
  },
  "_mentions": 2,
  "_devurl": "https://github.com/liubuntu/seqsqc",
  "_searchresults": 7,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/SeqSQC.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/liubuntu/seqsqc",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "gdsfile",
    "gdsfile<-",
    "IBDCheck",
    "IBDRemove",
    "Inbreeding",
    "LoadVfile",
    "MissingRate",
    "PCACheck",
    "plotQC",
    "problemList",
    "QCresult",
    "QCresult<-",
    "RenderReport",
    "sampleQC",
    "SeqOpen",
    "SeqSQC",
    "SexCheck"
  ],
  "_help": [
    {
      "page": "SeqSQC-package",
      "title": "Sample Quality Check for NGS Data using SeqSQC package",
      "topics": [
        "SeqSQC-package"
      ]
    },
    {
      "page": "CCDS.Hs37.3.reduced_chr1.bed",
      "title": "Example capture region file used in vignette.",
      "topics": [
        "CCDS.Hs37.3.reduced_chr1.bed"
      ]
    },
    {
      "page": "example_sub.vcf",
      "title": "Example vcf file used in vignette.",
      "topics": [
        "example_sub.vcf"
      ]
    },
    {
      "page": "example.gds",
      "title": "example gds file used in vignette.",
      "topics": [
        "example.gds"
      ]
    },
    {
      "page": "example.seqfile.Rdata",
      "title": "Example SeqSQC file used in vignette.",
      "topics": [
        "example.seqfile.Rdata"
      ]
    },
    {
      "page": "IBDCheck",
      "title": "Sample relationship check with SeqSQC object input file.",
      "topics": [
        "IBDCheck"
      ]
    },
    {
      "page": "IBDRemove",
      "title": "Obtain the problematic sample list from IBD relatedness.",
      "topics": [
        "IBDRemove"
      ]
    },
    {
      "page": "Inbreeding",
      "title": "Sample inbreeding check with SeqSQC object input file.",
      "topics": [
        "Inbreeding"
      ]
    },
    {
      "page": "LoadVfile",
      "title": "Data preprocessing for VCF or plink input from NGS or GWAS data.",
      "topics": [
        "LoadVfile"
      ]
    },
    {
      "page": "MissingRate",
      "title": "Sample missing rate check with SeqSQC object input file.",
      "topics": [
        "MissingRate"
      ]
    },
    {
      "page": "PCACheck",
      "title": "Population outlier check with SeqSQC object input file.",
      "topics": [
        "PCACheck"
      ]
    },
    {
      "page": "plotQC",
      "title": "Plot the QC results for specific QC steps.",
      "topics": [
        "plotQC"
      ]
    },
    {
      "page": "problemList",
      "title": "Generate the problematic sample list.",
      "topics": [
        "problemList"
      ]
    },
    {
      "page": "RenderReport",
      "title": "Render the rmarkdown file for generating a sample QC report.",
      "topics": [
        "RenderReport"
      ]
    },
    {
      "page": "sampleAnnotation.txt",
      "title": "Sample annotation file for the example data used in vignette.",
      "topics": [
        "sampleAnnotation.txt"
      ]
    },
    {
      "page": "sampleQC",
      "title": "The wrap-up function for sample QC of sequencing/GWAS data.",
      "topics": [
        "sampleQC"
      ]
    },
    {
      "page": "SeqOpen",
      "title": "Open the gds file in SeqSQC objects.",
      "topics": [
        "SeqOpen"
      ]
    },
    {
      "page": "SeqSQC-class",
      "title": "A data format to store genotype phenotype and sample QC results from SeqSQC.",
      "topics": [
        "\"gdsfile<-\",SeqSQC-method",
        "\"QCresult<-\",SeqSQC-method",
        "gdsfile",
        "gdsfile,SeqSQC-method",
        "gdsfile<-",
        "gdsfile<-,SeqSQC-method",
        "QCresult",
        "QCresult,SeqSQC-method",
        "QCresult<-",
        "QCresult<-,SeqSQC-method",
        "SeqSQC",
        "SeqSQC-class"
      ]
    },
    {
      "page": "SexCheck",
      "title": "Sample gender check with SeqSQC object input file.",
      "topics": [
        "SexCheck"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/SeqSQC/raw/HEAD/README.md",
  "_rundeps": [
    "AnnotationDbi",
    "AnnotationHub",
    "askpass",
    "base64enc",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocManager",
    "BiocVersion",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "bslib",
    "cachem",
    "class",
    "cli",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "digest",
    "dplyr",
    "e1071",
    "evaluate",
    "ExperimentHub",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "forcats",
    "fs",
    "gdsfmt",
    "generics",
    "GenomicRanges",
    "GGally",
    "ggplot2",
    "ggstats",
    "glue",
    "gtable",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httr",
    "httr2",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "later",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "MASS",
    "memoise",
    "mime",
    "openssl",
    "otel",
    "patchwork",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "png",
    "prettyunits",
    "progress",
    "promises",
    "proxy",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "reshape2",
    "RhpcBLASctl",
    "rlang",
    "rmarkdown",
    "RSQLite",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "SNPRelate",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "vignette.Rmd",
      "filename": "vignette.html",
      "title": "Sample Quality Check for NGS Data using SeqSQC package",
      "author": "Qian Liu, Qianqian Zhu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Quick start",
        "Data preparation",
        "Input data",
        "SeqSQC class",
        "GDS class",
        "Standard workflow",
        "Sample missing rate check",
        "Sex check",
        "Inbreeding check",
        "IBD check",
        "Population outlier check",
        "Summary of QC results",
        "Problematic sample list",
        "reporting of results",
        "How to get help for SeqSQC",
        "Session info"
      ],
      "created": "2017-08-24 19:08:57",
      "modified": "2018-08-30 17:56:16",
      "commits": 12
    }
  ],
  "_score": 5.079181246047625,
  "_indexed": true,
  "_nocasepkg": "seqsqc",
  "_universes": [
    "bioc",
    "liubuntu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.35.0",
      "date": "2026-05-30T10:24:22.000Z",
      "distro": "noble",
      "commit": "d08f6591c9eb065e3d75ba9c6be3fafed18e5340",
      "fileid": "3cfce120fa6feb9f74a38db57367a747a1484de28cb066ac842fe689a98b11a2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676991840"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.35.0",
      "date": "2026-05-30T10:24:16.000Z",
      "distro": "noble",
      "commit": "d08f6591c9eb065e3d75ba9c6be3fafed18e5340",
      "fileid": "977f294ae96bdb92464a0b457dc544c1ee07184541432c5b9e0d6560ce4ad93d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676991840"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.35.0",
      "date": "2026-05-30T14:37:57.000Z",
      "commit": "d08f6591c9eb065e3d75ba9c6be3fafed18e5340",
      "fileid": "37c9ea9e148f0f25a5a5848595e62f42cc258a54ec024964af68c01ae953cb74",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676991840"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.35.0",
      "date": "2026-05-30T14:37:44.000Z",
      "commit": "d08f6591c9eb065e3d75ba9c6be3fafed18e5340",
      "fileid": "d12f6c58b2edc5da37711ea22fe75a9a5715d16e2dc4a9c784c5be89a392fd48",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676991840"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.35.0",
      "date": "2026-05-30T10:23:43.000Z",
      "commit": "d08f6591c9eb065e3d75ba9c6be3fafed18e5340",
      "fileid": "ff5e53509f7af216590c9134af4e8ff41a73f398f37efd9cfd8f352215ca090b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676991840"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-05-30T10:22:17.000Z",
      "commit": "d08f6591c9eb065e3d75ba9c6be3fafed18e5340",
      "fileid": "567b6778a1db50d6554bbce44fb30998649dfdb448279770022a43ef6e9c0f17",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676991840"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-05-30T10:22:47.000Z",
      "commit": "d08f6591c9eb065e3d75ba9c6be3fafed18e5340",
      "fileid": "ddd790c7e464696edaddcc819371a63c6acc98f91d089f75c288d386898d117f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676991840"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-05-30T10:22:14.000Z",
      "commit": "d08f6591c9eb065e3d75ba9c6be3fafed18e5340",
      "fileid": "fcb6aa58fa4021c7adc704f2993dd1c326879135db5a6d29591e402cd36d977d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676991840"
    }
  ]
}