{
  "_id": "6ae33d2c327abcdf86866f5d",
  "Type": "Package",
  "Package": "BioGA",
  "Title": "Bioinformatics Genetic Algorithm (BioGA)",
  "Version": "1.7.0",
  "Authors@R": "person(\"Dany\", \"Mukesha\", , \"danymukesha@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0001-9514-751X\"))",
  "Description": "Genetic algorithm are a class of optimization algorithms\ninspired by the process of natural selection and genetics. This\npackage allows users to analyze and optimize high throughput\ngenomic data using genetic algorithms.  The functions provided\nare implemented in C++ for improved speed and efficiency, with\nan easy-to-use interface for use within R.",
  "License": "MIT + file LICENSE",
  "URL": "https://danymukesha.github.io/BioGA/",
  "BugReports": "https://github.com/danymukesha/BioGA/issues",
  "VignetteBuilder": "knitr",
  "biocViews": "ExperimentalDesign, Technology",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.1",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "cmake make libmagick++-dev gsfonts texlive\nlibuv1-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:03:19 UTC",
  "RemoteUrl": "https://github.com/bioc/BioGA",
  "RemoteRef": "HEAD",
  "RemoteSha": "4a2de1d1e3fc836ed0a40b54363c00d81a9741d9",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-29 11:20:16 UTC",
    "User": "root"
  },
  "Author": "Dany Mukesha [aut, cre] (ORCID:\n<https://orcid.org/0009-0001-9514-751X>)",
  "Maintainer": "Dany Mukesha <danymukesha@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "BioGA_1.7.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/6c592b1c6bf3e96de1b08648377ab9c333e7d85d6b1921f41636dbb6ffd3d658",
  "_filesize": 211381,
  "_sha256": "6c592b1c6bf3e96de1b08648377ab9c333e7d85d6b1921f41636dbb6ffd3d658",
  "_expires": "2027-02-06T12:33:45.000Z",
  "_created": "2026-10-29T11:20:16.000Z",
  "_published": "2026-10-29T12:33:47.880Z",
  "_upstream": "https://github.com/bioc/BioGA",
  "_status": "success",
  "_maintainer": {
    "name": "Dany Mukesha",
    "email": "danymukesha@gmail.com",
    "login": "danymukesha",
    "mastodon": "@dmukesha@mastodon.social",
    "bluesky": "@duseronx.bsky.social",
    "orcid": "0009-0001-9514-751X",
    "twitter": "@duseronx",
    "description": "",
    "uuid": 45208254
  },
  "_jobs": [
    {
      "job": 123416466423,
      "time": 179,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12893396483"
    },
    {
      "job": 123416466168,
      "time": 252,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12892908695"
    },
    {
      "job": 123416466165,
      "time": 361,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12893845742"
    },
    {
      "job": 123416466608,
      "time": 242,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12893830543"
    },
    {
      "job": 123416466108,
      "time": 394,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12894130204"
    },
    {
      "job": 123416466296,
      "time": 212,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12896522967"
    },
    {
      "job": 123416466290,
      "time": 665,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12897870905"
    },
    {
      "job": 123416466160,
      "time": 188,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12896831887"
    },
    {
      "job": 123416466268,
      "time": 380,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12896284972"
    },
    {
      "job": 123413070166,
      "time": 457,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12892499327"
    },
    {
      "job": 123416466118,
      "time": 149,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12892428996"
    },
    {
      "job": 123416466189,
      "time": 356,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12892469559"
    },
    {
      "job": 123416466209,
      "time": 281,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12892799201"
    },
    {
      "job": 123416466282,
      "time": 260,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12893451713"
    },
    {
      "job": 123416466255,
      "time": 370,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12894155246"
    },
    {
      "job": 123416466306,
      "time": 230,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12893895267"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 2
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/40863683635",
  "_commit": {
    "id": "4a2de1d1e3fc836ed0a40b54363c00d81a9741d9",
    "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": 1777381399
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "animation",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "biocViews",
      "role": "Imports"
    },
    {
      "package": "sessioninfo",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.7.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.6.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "experimentaldesign",
    "technology",
    "data-analysis",
    "gene-expression",
    "genetic-algorithms",
    "genomics",
    "optimization-algorithms",
    "cpp"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "danymukesha",
      "count": 107,
      "uuid": 45208254
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 481,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 278,
    "source": "https://www.bioconductor.org/packages/stats/bioc/BioGA"
  },
  "_devurl": "https://github.com/danymukesha/bioga",
  "_pkgdown": "https://danymukesha.github.io/BioGA/",
  "_searchresults": 0,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/BioGA.html",
    "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/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/danymukesha/bioga",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "crossover_cpp",
    "evaluate_fitness_cpp",
    "initialize_population_cpp",
    "mutation_cpp",
    "plot_fitness",
    "plot_fitness_history",
    "plot_population",
    "replacement_cpp",
    "selection_cpp"
  ],
  "_help": [
    {
      "page": "crossover_cpp",
      "title": "Function to perform crossover between selected individuals",
      "topics": [
        "crossover_cpp"
      ]
    },
    {
      "page": "evaluate_fitness_cpp",
      "title": "Function to evaluate fitness using genomic data",
      "topics": [
        "evaluate_fitness_cpp"
      ]
    },
    {
      "page": "initialize_population_cpp",
      "title": "Function to initialize the population from genomic data",
      "topics": [
        "initialize_population_cpp"
      ]
    },
    {
      "page": "mutation_cpp",
      "title": "Function to mutate the offspring",
      "topics": [
        "mutation_cpp"
      ]
    },
    {
      "page": "plot_fitness",
      "title": "Plot Fitness Values",
      "topics": [
        "plot_fitness"
      ]
    },
    {
      "page": "plot_fitness_history",
      "title": "Plot Fitness Change Over Generations",
      "topics": [
        "plot_fitness_history"
      ]
    },
    {
      "page": "plot_population",
      "title": "Plot Population Distribution",
      "topics": [
        "plot_population"
      ]
    },
    {
      "page": "replacement_cpp",
      "title": "Function to replace non-selected individuals in the population",
      "topics": [
        "replacement_cpp"
      ]
    },
    {
      "page": "selection_cpp",
      "title": "Function to select individuals based on fitness scores",
      "topics": [
        "selection_cpp"
      ]
    }
  ],
  "_pkglogo": "https://github.com/bioc/BioGA/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/bioc/BioGA/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "animation",
    "base64enc",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocManager",
    "BiocStyle",
    "biocViews",
    "bitops",
    "bookdown",
    "bslib",
    "cachem",
    "cli",
    "cpp11",
    "curl",
    "DelayedArray",
    "digest",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "graph",
    "gtable",
    "highr",
    "htmltools",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lattice",
    "lifecycle",
    "magick",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "R6",
    "rappdirs",
    "RBGL",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "rlang",
    "rmarkdown",
    "RUnit",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "sessioninfo",
    "SparseArray",
    "SummarizedExperiment",
    "tinytex",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "XVector",
    "yaml"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "Introduction.Rmd",
      "filename": "Introduction.html",
      "title": "Introduction",
      "author": "Dany Mukesha",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Getting Started",
        "Installation",
        "Overview",
        "Example Scenario",
        "Initialization",
        "Genetic Algorithm Optimization",
        "Fitness Calculation"
      ],
      "created": "2024-02-26 17:47:21",
      "modified": "2024-06-04 17:49:43",
      "commits": 7
    }
  ],
  "_score": 4,
  "_indexed": true,
  "_nocasepkg": "bioga",
  "_universes": [
    "bioc",
    "danymukesha"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.7.0",
      "date": "2026-10-29T11:23:27.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "4a2de1d1e3fc836ed0a40b54363c00d81a9741d9",
      "fileid": "https://r2.ropensci.org/76b1a71482e9964d49c1b0605a1052839e097fca9e7cd2c88ebf3705fb378c03",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40863683635"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.7.0",
      "date": "2026-10-29T11:24:33.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "4a2de1d1e3fc836ed0a40b54363c00d81a9741d9",
      "fileid": "https://r2.ropensci.org/ff5ddf7fce4b682b4e6c3accf805b80b6914bdf3c691e86acb98a5ae5f59e276",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40863683635"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.7.0",
      "date": "2026-10-29T11:23:23.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "4a2de1d1e3fc836ed0a40b54363c00d81a9741d9",
      "fileid": "https://r2.ropensci.org/8f605b6cb19b065e5a3c00c023cb0e0ad22a32028a0bac8017358adc29ba95f4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40863683635"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.7.0",
      "date": "2026-10-29T11:25:08.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "4a2de1d1e3fc836ed0a40b54363c00d81a9741d9",
      "fileid": "https://r2.ropensci.org/29f61d18316400da3dcd6069666711b4528549be706f00cc994702c7b4639759",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40863683635"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.7.0",
      "date": "2026-10-29T12:24:07.000Z",
      "arch": "aarch64",
      "commit": "4a2de1d1e3fc836ed0a40b54363c00d81a9741d9",
      "fileid": "https://r2.ropensci.org/4dbe1ca9b176d37748f49742eb06128af7ff6063d9d466e15243c917a7ac7eb8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40863683635"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.7.0",
      "date": "2026-10-29T12:27:47.000Z",
      "arch": "x86_64",
      "commit": "4a2de1d1e3fc836ed0a40b54363c00d81a9741d9",
      "fileid": "https://r2.ropensci.org/28e84acfad7539865214b5648c0829bc350abf99bea3dea78671664e978e4735",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40863683635"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.7.0",
      "date": "2026-10-29T12:23:56.000Z",
      "arch": "aarch64",
      "commit": "4a2de1d1e3fc836ed0a40b54363c00d81a9741d9",
      "fileid": "https://r2.ropensci.org/4167599c737b7040c47401c75da86fa5e51f46cf1b56269094b633bc8927587f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40863683635"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.7.0",
      "date": "2026-10-29T12:24:26.000Z",
      "arch": "x86_64",
      "commit": "4a2de1d1e3fc836ed0a40b54363c00d81a9741d9",
      "fileid": "https://r2.ropensci.org/6fc5bd75fd6aa8852a8b070f396a6bf24da370d9d2b006908d5571326355741a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40863683635"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.7.0",
      "date": "2026-10-29T11:23:24.000Z",
      "arch": "emscripten",
      "commit": "4a2de1d1e3fc836ed0a40b54363c00d81a9741d9",
      "fileid": "https://r2.ropensci.org/4846326fb0b9589bb6a404d4a5f2a1c5bd7b49fadd219fac20bc32004c30660b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40863683635"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-10-29T11:24:28.000Z",
      "arch": "aarch64",
      "commit": "4a2de1d1e3fc836ed0a40b54363c00d81a9741d9",
      "fileid": "https://r2.ropensci.org/abb3d71113107b2bd36bd716400f4c180263882720d79fb4769140366745aed9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40863683635"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-10-29T11:22:19.000Z",
      "arch": "x86_64",
      "commit": "4a2de1d1e3fc836ed0a40b54363c00d81a9741d9",
      "fileid": "https://r2.ropensci.org/287c364792c0f2192ab71a37f5e5decbbfbb3c78121e0008f23372d3cccc5b1d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40863683635"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-10-29T11:22:41.000Z",
      "arch": "x86_64",
      "commit": "4a2de1d1e3fc836ed0a40b54363c00d81a9741d9",
      "fileid": "https://r2.ropensci.org/dea5debfa45ef0bed1cac969737a758af231290aad1de77849f5ccfbaf48aa33",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40863683635"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-10-29T11:24:53.000Z",
      "arch": "aarch64",
      "commit": "4a2de1d1e3fc836ed0a40b54363c00d81a9741d9",
      "fileid": "https://r2.ropensci.org/c490da6a823e401bb85628ef70f3afaae01acd4cc69acd000a65a35e7ceee9e3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40863683635"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-10-29T11:22:20.000Z",
      "arch": "x86_64",
      "commit": "4a2de1d1e3fc836ed0a40b54363c00d81a9741d9",
      "fileid": "https://r2.ropensci.org/0cd290ab5585eaced1a4a202bcf8587a1de83e833514f9912f7aa51ebed2406c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40863683635"
    }
  ]
}