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  "Package": "genBaRcode",
  "Title": "Analysis and Visualization Tools for Genetic Barcode Data",
  "Version": "1.2.8",
  "Authors@R": "person(given = \"Lars\", family = \"Thielecke\", role = c(\"aut\", \"cre\"), \nemail = \"lars.thielecke@tu-dresden.de\")",
  "Description": "Provides the necessary functions to identify and extract a\nselection of already available barcode constructs (Cornils, K.\net al. (2014) <doi:10.1093/nar/gku081>) and freely choosable\nbarcode designs from next generation sequence (NGS) data.\nFurthermore, it offers the possibility to account for sequence\nerrors, the calculation of barcode similarities and provides a\nvariety of visualisation tools (Thielecke, L. et al. (2017)\n<doi:10.1038/srep43249>).",
  "License": "LGPL",
  "Encoding": "UTF-8",
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  "Collate": "'BCdata-class.R' 'BCdata-class-methods.R'\n'analysis_functions.R' 'data.R' 'error_correction_function.R'\n'helper_functions.R' 'plot_functions.R' 'raw_data_processing.R'",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-28 14:52:16 UTC",
    "User": "root"
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  "Author": "Lars Thielecke [aut, cre]",
  "Maintainer": "Lars Thielecke <lars.thielecke@tu-dresden.de>",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libbz2-dev libicu-dev\nlibjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev\nxz-utils zlib1g-dev",
  "Repository": "https://grafxzahl.r-universe.dev",
  "Date/Publication": "2025-03-10 15:32:49 UTC",
  "RemoteUrl": "https://github.com/cran/genBaRcode",
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  "_created": "2026-05-28T14:52:16.000Z",
  "_published": "2026-05-28T15:18:57.644Z",
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  "_buildurl": "https://github.com/r-universe/grafxzahl/actions/runs/26581839903",
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  "_host": "GitHub-Actions",
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    "author": "Lars Thielecke <lars.thielecke@tu-dresden.de>",
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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    "manual.pdf"
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  "_releases": [
    {
      "version": "1.0.0",
      "date": "2017-09-21"
    },
    {
      "version": "1.1.0",
      "date": "2018-08-10"
    },
    {
      "version": "1.2.0",
      "date": "2019-07-08"
    },
    {
      "version": "1.2.2",
      "date": "2019-10-25"
    },
    {
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  "_exports": [
    "asBCdat",
    "com_pair",
    "createGDF",
    "error_correction_circlePlot",
    "error_correction_clustered_HDs",
    "error_correction_treePlot",
    "errorCorrection",
    "extractBarcodes",
    "genBaRcode_app",
    "generateKirchenplot",
    "generateTimeSeriesData",
    "getBackbone",
    "getBackboneSelection",
    "getLabel",
    "getReads",
    "getResultsDir",
    "ggplotDistanceGraph",
    "ggplotDistanceGraph_EC",
    "hybridsIdentification",
    "plotClusterGgTree",
    "plotClusterTree",
    "plotDistanceIgraph",
    "plotDistanceVisNetwork",
    "plotDistanceVisNetwork_EC",
    "plotNucFrequency",
    "plotQualityScoreDis",
    "plotQualityScorePerCycle",
    "plotReadFrequencies",
    "plotSeqLogo",
    "plotTimeSeries",
    "plotVennDiagram",
    "processingRawData",
    "qualityFiltering",
    "readBCdat",
    "setBackbone",
    "setLabel",
    "setReads",
    "setResultsDir"
  ],
  "_datasets": [
    {
      "name": "BC_dat",
      "title": "Barcode distribution of an example experiment.",
      "object": "BC_dat",
      "class": [
        "BCdat"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "BC_dat_EC",
      "title": "Barcode distribution of an example experiment.",
      "object": "BC_dat_EC",
      "class": [
        "BCdat"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "dot-createPatternFile",
      "title": "Internal function",
      "topics": [
        ".createPatternFile"
      ]
    },
    {
      "page": "dot-generateColors",
      "title": "Color list generation",
      "topics": [
        ".generateColors"
      ]
    },
    {
      "page": "dot-getBarcodeFilter",
      "title": "Internal function",
      "topics": [
        ".getBarcodeFilter"
      ]
    },
    {
      "page": "dot-getDiagonalIndex",
      "title": "Index Generation",
      "topics": [
        ".getDiagonalIndex"
      ]
    },
    {
      "page": "dot-getMinDist",
      "title": "Distance calculation",
      "topics": [
        ".getMinDist"
      ]
    },
    {
      "page": "dot-getWobblePos",
      "title": "getWobblePos",
      "topics": [
        ".getWobblePos"
      ]
    },
    {
      "page": "dot-hex2rgbColor",
      "title": "Converts hex colors into gephi usable rgb colors",
      "topics": [
        ".hex2rgbColor"
      ]
    },
    {
      "page": "dot-revComp",
      "title": "DNA string manipulation",
      "topics": [
        ".revComp"
      ]
    },
    {
      "page": "dot-revComp_EqLength",
      "title": "DNA string manipulation for equal string sizes",
      "topics": [
        ".revComp_EqLength"
      ]
    },
    {
      "page": "dot-revComp_UneqLength",
      "title": "DNA string manipulation for unequal string sizes",
      "topics": [
        ".revComp_UneqLength"
      ]
    },
    {
      "page": "dot-testDirIdentifier",
      "title": "Internal function",
      "topics": [
        ".testDirIdentifier"
      ]
    },
    {
      "page": "asBCdat",
      "title": "Data Type Conversion",
      "topics": [
        "asBCdat"
      ]
    },
    {
      "page": "BC_dat",
      "title": "Barcode distribution of an example experiment.",
      "topics": [
        "BC_dat"
      ]
    },
    {
      "page": "BC_dat_EC",
      "title": "Barcode distribution of an example experiment.",
      "topics": [
        "BC_dat_EC"
      ]
    },
    {
      "page": "BCdat-class",
      "title": "BCdat class.",
      "topics": [
        "BCdat",
        "BCdat-class"
      ]
    },
    {
      "page": "com_pair",
      "title": "Compairing two BCdat Objects",
      "topics": [
        "com_pair"
      ]
    },
    {
      "page": "createGDF",
      "title": "Creating a gdf File",
      "topics": [
        "createGDF"
      ]
    },
    {
      "page": "error_correction_circlePlot",
      "title": "Circle Plot",
      "topics": [
        "error_correction_circlePlot"
      ]
    },
    {
      "page": "error_correction_clustered_HDs",
      "title": "Clustered HD Plot",
      "topics": [
        "error_correction_clustered_HDs"
      ]
    },
    {
      "page": "error_correction_treePlot",
      "title": "Tree Plot",
      "topics": [
        "error_correction_treePlot"
      ]
    },
    {
      "page": "errorCorrection",
      "title": "Error Correction",
      "topics": [
        "errorCorrection"
      ]
    },
    {
      "page": "extractBarcodes",
      "title": "Barcode extraction",
      "topics": [
        "extractBarcodes"
      ]
    },
    {
      "page": "genBaRcode_app",
      "title": "Shiny App",
      "topics": [
        "genBaRcode_app"
      ]
    },
    {
      "page": "generateKirchenplot",
      "title": "Plotting a Kirchenplot",
      "topics": [
        "generateKirchenplot"
      ]
    },
    {
      "page": "generateTimeSeriesData",
      "title": "Generating Time Series Data Object",
      "topics": [
        "generateTimeSeriesData"
      ]
    },
    {
      "page": "getBackbone",
      "title": "Accessing the Barcode Backbone slot of a BCdat objects.",
      "topics": [
        "getBackbone"
      ]
    },
    {
      "page": "getBackboneSelection",
      "title": "Predefined Barcode Backbone Sequences",
      "topics": [
        "getBackboneSelection"
      ]
    },
    {
      "page": "getLabel",
      "title": "Accessing the Label slot of a BCdat objects.",
      "topics": [
        "getLabel"
      ]
    },
    {
      "page": "getReads",
      "title": "Accessing the Read-Count slot of a BCdat objects.",
      "topics": [
        "getReads"
      ]
    },
    {
      "page": "getResultsDir",
      "title": "Accessing the Results Directory slot of a BCdat objects.",
      "topics": [
        "getResultsDir"
      ]
    },
    {
      "page": "ggplotDistanceGraph",
      "title": "Plotting a Distance Network",
      "topics": [
        "ggplotDistanceGraph"
      ]
    },
    {
      "page": "ggplotDistanceGraph_EC",
      "title": "Plotting a Distance Network (error correction)",
      "topics": [
        "ggplotDistanceGraph_EC"
      ]
    },
    {
      "page": "hybridsIdentification",
      "title": "Identifies hybrid barcodes",
      "topics": [
        "hybridsIdentification"
      ]
    },
    {
      "page": "plotClusterGgTree",
      "title": "Plotting a Cluster ggTree",
      "topics": [
        "plotClusterGgTree"
      ]
    },
    {
      "page": "plotClusterTree",
      "title": "Plotting a Cluster Tree",
      "topics": [
        "plotClusterTree"
      ]
    },
    {
      "page": "plotDistanceIgraph",
      "title": "Plotting a Distance Network",
      "topics": [
        "plotDistanceIgraph"
      ]
    },
    {
      "page": "plotDistanceVisNetwork",
      "title": "Plotting a Distance Network",
      "topics": [
        "plotDistanceVisNetwork"
      ]
    },
    {
      "page": "plotDistanceVisNetwork_EC",
      "title": "Plotting a Distance Network (error correction)",
      "topics": [
        "plotDistanceVisNetwork_EC"
      ]
    },
    {
      "page": "plotNucFrequency",
      "title": "Plotting Nucleotide Frequency",
      "topics": [
        "plotNucFrequency"
      ]
    },
    {
      "page": "plotQualityScoreDis",
      "title": "Plotting Quality Score Distribution",
      "topics": [
        "plotQualityScoreDis"
      ]
    },
    {
      "page": "plotQualityScorePerCycle",
      "title": "Plotting Quality Score per Cycle",
      "topics": [
        "plotQualityScorePerCycle"
      ]
    },
    {
      "page": "plotReadFrequencies",
      "title": "Plotting a Barplot",
      "topics": [
        "plotReadFrequencies"
      ]
    },
    {
      "page": "plotSeqLogo",
      "title": "Plots a sequence logo",
      "topics": [
        "plotSeqLogo"
      ]
    },
    {
      "page": "plotTimeSeries",
      "title": "Plotting Time Series Data",
      "topics": [
        "plotTimeSeries"
      ]
    },
    {
      "page": "plotVennDiagram",
      "title": "Plotting a VennDiagram",
      "topics": [
        "plotVennDiagram"
      ]
    },
    {
      "page": "prepareDatObject",
      "title": "Data Object Preparation",
      "topics": [
        "prepareDatObject"
      ]
    },
    {
      "page": "processingRawData",
      "title": "Data processing",
      "topics": [
        "processingRawData"
      ]
    },
    {
      "page": "qualityFiltering",
      "title": "Quality Filtering",
      "topics": [
        "qualityFiltering"
      ]
    },
    {
      "page": "readBCdat",
      "title": "Data Input",
      "topics": [
        "readBCdat"
      ]
    },
    {
      "page": "setBackbone",
      "title": "Replacing the Barcode Backbone slot of a BCdat objects.",
      "topics": [
        "setBackbone"
      ]
    },
    {
      "page": "setLabel",
      "title": "Replacing the Label slot of a BCdat objects.",
      "topics": [
        "setLabel"
      ]
    },
    {
      "page": "setReads",
      "title": "Replacing the Read-Count slot of a BCdat objects.",
      "topics": [
        "setReads"
      ]
    },
    {
      "page": "setResultsDir",
      "title": "Replacing the Results Directory slot of a BCdat objects.",
      "topics": [
        "setResultsDir"
      ]
    }
  ],
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    "BH",
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    "phangorn",
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    "pkgconfig",
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    "promises",
    "purrr",
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    "quadprog",
    "R6",
    "rappdirs",
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    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
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    "Rhtslib",
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    "rmarkdown",
    "Rsamtools",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
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    "sna",
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    "sourcetools",
    "SparseArray",
    "statnet.common",
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    "tibble",
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  "_vignettes": [
    {
      "source": "genBaRcode_Vignette.Rmd",
      "filename": "genBaRcode_Vignette.html",
      "title": "Introduction to genBaRcode",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Table of Contents",
        "[1. genBaRcode Package][]",
        "[2. Barcode Extraction][]",
        "[3. Error Correction][]",
        "[4. Visualizations][]",
        "[5. Generating and plotting Time Series Data][]",
        "[6. genBaRcode Shiny-App][]",
        "[7. Miscellaneous Functions][]",
        "1. genBaRcode Package",
        "2. Barcode Extraction",
        "2.1 Parallelization",
        "2.2 Manipulating the BCdat data type",
        "2.3 Reading and Converting other data formats",
        "3. Error Correction",
        "3.1 Error Correction Approaches",
        "3.1.1 Standard",
        "3.1.2 Graph based",
        "3.1.3 Connectivity based",
        "3.1.4 Clustering",
        "4. Visualizations",
        "4.1 Fastq Quality Plots",
        "4.2 Plotting Barcode Frequencies",
        "4.3 Plotting Barcode Relations",
        "4.4 Plotting Error Correction Results",
        "5. Generating and plotting Time Series Data",
        "6. genBaRcode Shiny-App",
        "7. Miscellaneous Functions"
      ],
      "created": "2019-10-25 14:10:02",
      "modified": "2019-10-25 14:10:02",
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      "title": "Introduction to the genBaRcode GUI",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2019-10-25 14:10:02",
      "modified": "2019-10-25 14:10:02",
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