{
  "_id": "6a1141eaacfb0bcc41ce69d7",
  "Package": "rKOMICS",
  "Title": "Minicircle Sequence Cluster (MSC) Analyses",
  "Version": "1.2",
  "Date": "2021-07-26",
  "Authors@R": "c(person(\"Frederik\", \"Van den Broeck\", role = c(\"aut\"),\nemail = \"frederik.vandenbroeck@kuleuven.be\"),\nperson(\"Manon\", \"Geerts\", role = c(\"aut\", \"cre\"), email = \"mgeerts@itg.be\") )",
  "Description": "It establishes a critical framework to manipulate, explore\nand extract biologically relevant information from\nmitochondrial minicircle assemblies in tens to hundreds of\nsamples simultaneously and efficiently. This should facilitate\nresearch that aims to develop new molecular markers for\nidentifying species-specific minicircles, or to study the\nancestry of parasites for complementary insights into their\nevolutionary history.",
  "License": "GPL",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.1.1",
  "biocViews": "",
  "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev perl",
  "Repository": "https://geertsmanon.r-universe.dev",
  "Date/Publication": "2021-09-12 17:41:34 UTC",
  "RemoteUrl": "https://github.com/geertsmanon/rkomics",
  "RemoteRef": "HEAD",
  "RemoteSha": "a51234afd2df5646bc751297c384856004bff6f9",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-23 05:53:03 UTC",
    "User": "root"
  },
  "Author": "Frederik Van den Broeck [aut],\nManon Geerts [aut, cre]",
  "Maintainer": "Manon Geerts <mgeerts@itg.be>",
  "MD5sum": "d56728f2ce09c263391aea6e94319beb",
  "_user": "geertsmanon",
  "_type": "src",
  "_file": "rKOMICS_1.2.tar.gz",
  "_fileid": "9e1eec9c82a238b91c86a64a5198fc9d7d687a606146f615f4783d58e9776b54",
  "_filesize": 5582244,
  "_sha256": "9e1eec9c82a238b91c86a64a5198fc9d7d687a606146f615f4783d58e9776b54",
  "_created": "2026-05-23T05:53:03.000Z",
  "_published": "2026-05-23T05:58:02.112Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77501276782,
      "time": 232,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7174731425"
    },
    {
      "job": 77501276788,
      "time": 217,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7174730002"
    },
    {
      "job": 77501276793,
      "time": 223,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7174727105"
    },
    {
      "job": 77501276795,
      "time": 166,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7174722400"
    },
    {
      "job": 77501026790,
      "time": 287,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7174707045"
    },
    {
      "job": 77501276772,
      "time": 174,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7174725461"
    },
    {
      "job": 77501276778,
      "time": 159,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7174723804"
    },
    {
      "job": 77501276789,
      "time": 182,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7174726247"
    },
    {
      "job": 77501276780,
      "time": 172,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7174725854"
    }
  ],
  "_buildurl": "https://github.com/r-universe/geertsmanon/actions/runs/26325013795",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/geertsmanon/rkomics",
  "_commit": {
    "id": "a51234afd2df5646bc751297c384856004bff6f9",
    "author": "GeertsManon <87172678+GeertsManon@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Add files via upload",
    "time": 1631468494
  },
  "_maintainer": {
    "name": "Manon Geerts",
    "email": "mgeerts@itg.be"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "circlize",
      "role": "Imports"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "factoextra",
      "role": "Imports"
    },
    {
      "package": "FactoMineR",
      "role": "Imports"
    },
    {
      "package": "ggpubr",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "viridis",
      "role": "Suggests"
    }
  ],
  "_owner": "geertsmanon",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "geertsmanon",
      "count": 14,
      "uuid": 87172678
    }
  ],
  "_userbio": {
    "uuid": 87172678,
    "type": "user",
    "name": "GeertsManon"
  },
  "_downloads": {
    "count": 248,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rKOMICS"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/geertsmanon/rkomics",
  "_searchresults": 2,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/rKOMICS.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/geertsmanon/rkomics",
  "_realowner": "geertsmanon",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0",
      "date": "2021-02-17"
    },
    {
      "version": "1.1",
      "date": "2021-07-21"
    },
    {
      "version": "1.2",
      "date": "2023-06-18"
    },
    {
      "version": "1.3",
      "date": "2023-06-30"
    }
  ],
  "_exports": [
    "%>%",
    "msc.depth",
    "msc.heatmap",
    "msc.length",
    "msc.matrix",
    "msc.pca",
    "msc.quality",
    "msc.richness",
    "msc.seqs",
    "msc.similarity",
    "msc.subset",
    "msc.uc",
    "preprocess",
    "read.uc"
  ],
  "_datasets": [
    {
      "name": "exData",
      "title": "Example dataset",
      "object": "exData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "matrices",
      "title": "Example cluster matrices",
      "object": "matrices",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "exData",
      "title": "Example dataset",
      "topics": [
        "exData"
      ]
    },
    {
      "page": "matrices",
      "title": "Example cluster matrices",
      "topics": [
        "matrices"
      ]
    },
    {
      "page": "msc.depth",
      "title": "Check the read depth of assembled minicircles",
      "topics": [
        "msc.depth"
      ]
    },
    {
      "page": "msc.heatmap",
      "title": "Visualization of cluster matrices",
      "topics": [
        "msc.heatmap"
      ]
    },
    {
      "page": "msc.length",
      "title": "Length of minicircles",
      "topics": [
        "msc.length"
      ]
    },
    {
      "page": "msc.matrix",
      "title": "Build cluster matrix",
      "topics": [
        "msc.matrix"
      ]
    },
    {
      "page": "msc.pca",
      "title": "Prinicple Component Analysis based on MSC",
      "topics": [
        "msc.pca"
      ]
    },
    {
      "page": "msc.quality",
      "title": "Check the quality of the assembly",
      "topics": [
        "msc.quality"
      ]
    },
    {
      "page": "msc.richness",
      "title": "Minicircle Sequence Cluster richness",
      "topics": [
        "msc.richness"
      ]
    },
    {
      "page": "msc.seqs",
      "title": "Retrieve sequences",
      "topics": [
        "msc.seqs"
      ]
    },
    {
      "page": "msc.similarity",
      "title": "Minicircle Sequence Cluster similarity",
      "topics": [
        "msc.similarity"
      ]
    },
    {
      "page": "msc.subset",
      "title": "Specific MSC",
      "topics": [
        "msc.subset"
      ]
    },
    {
      "page": "msc.uc",
      "title": "Cluster Analyses",
      "topics": [
        "msc.uc"
      ]
    },
    {
      "page": "preprocess",
      "title": "Filtering of minicircle sequences",
      "topics": [
        "preprocess"
      ]
    },
    {
      "page": "read.uc",
      "title": "Read in uc files",
      "topics": [
        "read.uc"
      ]
    },
    {
      "page": "rKOMICS",
      "title": "Minicircle Sequence Cluster (MSC) Analyses",
      "topics": [
        "rKOMICS"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "ape",
    "backports",
    "base64enc",
    "BiocGenerics",
    "boot",
    "broom",
    "bslib",
    "cachem",
    "car",
    "carData",
    "circlize",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "ComplexHeatmap",
    "corrplot",
    "cowplot",
    "cpp11",
    "crayon",
    "crosstalk",
    "dendextend",
    "Deriv",
    "digest",
    "doBy",
    "doParallel",
    "dplyr",
    "DT",
    "ellipse",
    "emmeans",
    "estimability",
    "evaluate",
    "factoextra",
    "FactoMineR",
    "farver",
    "fastmap",
    "flashClust",
    "fontawesome",
    "foreach",
    "forecast",
    "Formula",
    "fracdiff",
    "fs",
    "generics",
    "GetoptLong",
    "ggplot2",
    "ggpubr",
    "ggrepel",
    "ggsci",
    "ggsignif",
    "GlobalOptions",
    "glue",
    "gridExtra",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "leaps",
    "lifecycle",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixModels",
    "matrixStats",
    "memoise",
    "mgcv",
    "microbenchmark",
    "mime",
    "minqa",
    "modelr",
    "multcompView",
    "mvtnorm",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "otel",
    "pbkrtest",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "polynom",
    "promises",
    "purrr",
    "quantreg",
    "R6",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "reshape2",
    "rjson",
    "rlang",
    "rmarkdown",
    "rstatix",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "scatterplot3d",
    "shape",
    "SparseM",
    "stringi",
    "stringr",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "tinytex",
    "urca",
    "utf8",
    "vctrs",
    "viridis",
    "viridisLite",
    "withr",
    "xfun",
    "yaml",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "example.Rnw",
      "filename": "example.pdf",
      "title": "Application example",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2021-09-12 17:41:34",
      "modified": "2021-09-12 17:41:34",
      "commits": 1
    }
  ],
  "_score": 3,
  "_indexed": true,
  "_nocasepkg": "rkomics",
  "_universes": [
    "geertsmanon"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2",
      "date": "2026-05-23T05:56:18.000Z",
      "distro": "noble",
      "commit": "a51234afd2df5646bc751297c384856004bff6f9",
      "fileid": "c4c2475f83441c593cbabdcb18980937222e810c7a7aef7f8ecbee5851d59019",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/geertsmanon/actions/runs/26325013795"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.2",
      "date": "2026-05-23T05:56:08.000Z",
      "distro": "noble",
      "commit": "a51234afd2df5646bc751297c384856004bff6f9",
      "fileid": "de53e3033a639a095935f92257034cae977c5473414a1f4d8067c6671c19a182",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/geertsmanon/actions/runs/26325013795"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2",
      "date": "2026-05-23T05:55:57.000Z",
      "commit": "a51234afd2df5646bc751297c384856004bff6f9",
      "fileid": "a2126926133d849c4a71ce6773f0059b4dcb3e4b99541cdcf81c4ec555edbb71",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/geertsmanon/actions/runs/26325013795"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.2",
      "date": "2026-05-23T05:55:25.000Z",
      "commit": "a51234afd2df5646bc751297c384856004bff6f9",
      "fileid": "a9424b73eb8ae8d0fcea5aa4185dae43b764cc861d60b054069a43ac2fe00354",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/geertsmanon/actions/runs/26325013795"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.2",
      "date": "2026-05-23T05:56:24.000Z",
      "commit": "a51234afd2df5646bc751297c384856004bff6f9",
      "fileid": "73356966d6138c5895de43c2c2c9d50f61d8779520c2ddefc1ba9e560e09d68f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/geertsmanon/actions/runs/26325013795"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.2",
      "date": "2026-05-23T05:54:55.000Z",
      "commit": "a51234afd2df5646bc751297c384856004bff6f9",
      "fileid": "33f9def907a0957cba38729eedcb8d26208838b950454529263de218c5c759fa",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/geertsmanon/actions/runs/26325013795"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.2",
      "date": "2026-05-23T05:55:05.000Z",
      "commit": "a51234afd2df5646bc751297c384856004bff6f9",
      "fileid": "1777b0f9986f66a3d873d47d873f0e0d7981bc328a5c12cb82d167f2177f6420",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/geertsmanon/actions/runs/26325013795"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.2",
      "date": "2026-05-23T05:55:14.000Z",
      "commit": "a51234afd2df5646bc751297c384856004bff6f9",
      "fileid": "3b2f1e514ac7f98f884254552f3e0f57a1df132ce87c77a13a20dd10c3010359",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/geertsmanon/actions/runs/26325013795"
    }
  ]
}