{
  "_id": "6a1045e7acfb0bcc41c9e91e",
  "Package": "baseq",
  "Title": "Basic Sequence Processing Tool for Biological Data",
  "Version": "0.2.0",
  "Authors@R": "c(\nperson(\"Ambu\", \"Vijayan\", , \"ambuvjyn@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-8924-5685\")),\nperson(\"J.\", \"Sreekumar\", email = \"Sreekumar.J@icar.gov.in\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-4253-6378\", \"Principal Scientist, ICAR - Central Tuber Crops Research Institute\")))",
  "Description": "Primarily created as an easy and understanding way to do\nbasic sequences surrounding the central dogma of molecular\nbiology.",
  "License": "GPL-3",
  "URL": "https://github.com/ambuvjyn/baseq",
  "BugReports": "https://github.com/ambuvjyn/baseq/issues",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "LazyData": "true",
  "NeedsCompilation": "no",
  "Author": "Ambu Vijayan [aut, cre]\n(<https://orcid.org/0000-0001-8924-5685>), J. Sreekumar [aut]\n(<https://orcid.org/0000-0002-4253-6378>, Principal Scientist,\nICAR - Central Tuber Crops Research Institute)",
  "Maintainer": "Ambu Vijayan <ambuvjyn@gmail.com>",
  "Repository": "https://ambuvjyn.r-universe.dev",
  "Date/Publication": "2026-03-11 22:33:29 UTC",
  "RemoteUrl": "https://github.com/ambuvjyn/baseq",
  "RemoteRef": "HEAD",
  "RemoteSha": "fc12ff769ab08f6467ea4c17b69bdb80a85b198e",
  "Packaged": {
    "Date": "2026-05-11 05:45:41 UTC",
    "User": "root"
  },
  "MD5sum": "70f636df4b6a25e5996b14d1e5a53951",
  "_user": "ambuvjyn",
  "_type": "src",
  "_file": "baseq_0.2.0.tar.gz",
  "_fileid": "761d9dac10ba1a0b1b9c1713d00943a3c6b4aa528de587b2b9c5b048b1e5196c",
  "_filesize": 178339,
  "_sha256": "761d9dac10ba1a0b1b9c1713d00943a3c6b4aa528de587b2b9c5b048b1e5196c",
  "_created": "2026-05-11T05:45:41.000Z",
  "_published": "2026-06-10T10:33:23.228Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77375459921,
      "time": 115,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6911166463"
    },
    {
      "job": 77375459597,
      "time": 165,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6911175958"
    },
    {
      "job": 77375459670,
      "time": 192,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6911175345"
    },
    {
      "job": 77375459973,
      "time": 122,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6911163710"
    },
    {
      "job": 77375459359,
      "time": 179,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6911143321"
    },
    {
      "job": 77375459264,
      "time": 119,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7159998874"
    },
    {
      "job": 77375459465,
      "time": 87,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6911160715"
    },
    {
      "job": 77375460003,
      "time": 78,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6911159064"
    },
    {
      "job": 77375460100,
      "time": 97,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6911162899"
    }
  ],
  "_buildurl": "https://github.com/r-universe/ambuvjyn/actions/runs/25652524480",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/ambuvjyn/baseq",
  "_commit": {
    "id": "fc12ff769ab08f6467ea4c17b69bdb80a85b198e",
    "author": "Ambu Vijayan <ambuvjyn@gmail.com>",
    "committer": "Ambu Vijayan <ambuvjyn@gmail.com>",
    "message": "Final cleanup of v0.2.0: Removed redundant files and updated documentation\n",
    "time": 1773268409
  },
  "_maintainer": {
    "name": "Ambu Vijayan",
    "email": "ambuvjyn@gmail.com",
    "login": "ambuvjyn",
    "linkedin": "in/ambuvijayan",
    "uuid": 82611533,
    "orcid": "0000-0001-8924-5685"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "Biostrings",
      "role": "Suggests"
    }
  ],
  "_owner": "ambuvjyn",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-11",
      "n": 3
    }
  ],
  "_tags": [
    {
      "name": "V.0.2.0",
      "date": "2026-03-11"
    }
  ],
  "_topics": [
    "bioinformatics",
    "sequencing"
  ],
  "_stars": 4,
  "_contributors": [
    {
      "user": "ambuvjyn",
      "count": 27,
      "uuid": 82611533
    }
  ],
  "_userbio": {
    "uuid": 82611533,
    "type": "user",
    "name": "Ambu Vijayan",
    "description": "Passion for Bioinformatics, Biotechnology, Molecular biology, Computational Biology and Statistics "
  },
  "_downloads": {
    "count": 304,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/baseq"
  },
  "_devurl": "https://github.com/ambuvjyn/baseq",
  "_searchresults": 5,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/baseq.html",
    "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",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ambuvjyn/baseq",
  "_realowner": "ambuvjyn",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2023-03-22"
    },
    {
      "version": "0.1.1",
      "date": "2023-04-26"
    },
    {
      "version": "0.1.2",
      "date": "2023-04-28"
    },
    {
      "version": "0.1.4",
      "date": "2023-05-03"
    },
    {
      "version": "0.2.0",
      "date": "2026-03-11"
    }
  ],
  "_exports": [
    "as_baseq_dna",
    "as_baseq_rna",
    "as_Biostrings",
    "calculate_assembly_stats",
    "calculate_charge",
    "calculate_codon_usage",
    "calculate_identity",
    "calculate_mw",
    "calculate_pi",
    "calculate_tm",
    "clean_file",
    "clean_seq",
    "count_bases",
    "count_kmers",
    "count_pattern",
    "dna_to_protein",
    "dna_to_rna",
    "fastq_to_fasta",
    "filter_fastq_quality",
    "find_cpg_islands",
    "find_longest_orf",
    "gc_content",
    "get_genetic_code",
    "plot_aa_composition",
    "plot_dotplot",
    "plot_gc_skew",
    "plot_hydrophobicity",
    "read_seq",
    "rev_comp",
    "reverse_translate",
    "rna_to_dna",
    "rna_to_protein",
    "search_motif",
    "shuffle_sequence",
    "simulate_digestion",
    "simulate_fasta",
    "simulate_fastq",
    "simulate_pcr",
    "simulate_sequence",
    "summarize_fasta",
    "translate",
    "write_seq"
  ],
  "_datasets": [
    {
      "name": "sars_fragment",
      "title": "SARS-CoV-2 Genome Fragment",
      "object": "sars_fragment",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "as_baseq_dna",
      "title": "S3 DNA Class",
      "topics": [
        "as_baseq_dna"
      ]
    },
    {
      "page": "as_baseq_rna",
      "title": "S3 RNA Class",
      "topics": [
        "as_baseq_rna"
      ]
    },
    {
      "page": "as_Biostrings",
      "title": "Bioconductor Bridge",
      "topics": [
        "as_Biostrings"
      ]
    },
    {
      "page": "calculate_assembly_stats",
      "title": "Assembly Stats",
      "topics": [
        "calculate_assembly_stats"
      ]
    },
    {
      "page": "calculate_charge",
      "title": "Protein Net Charge",
      "topics": [
        "calculate_charge"
      ]
    },
    {
      "page": "calculate_codon_usage",
      "title": "Codon Usage RSCU",
      "topics": [
        "calculate_codon_usage"
      ]
    },
    {
      "page": "calculate_identity",
      "title": "Sequence Identity",
      "topics": [
        "calculate_identity"
      ]
    },
    {
      "page": "calculate_mw",
      "title": "Protein MW",
      "topics": [
        "calculate_mw"
      ]
    },
    {
      "page": "calculate_pi",
      "title": "Protein pI",
      "topics": [
        "calculate_pi"
      ]
    },
    {
      "page": "calculate_tm",
      "title": "Primer Tm",
      "topics": [
        "calculate_tm"
      ]
    },
    {
      "page": "clean_file",
      "title": "Batch File Cleaner",
      "topics": [
        "clean_file"
      ]
    },
    {
      "page": "clean_seq",
      "title": "Universal Sequence Cleaner",
      "topics": [
        "clean_seq"
      ]
    },
    {
      "page": "count_bases",
      "title": "Count Bases",
      "topics": [
        "count_bases"
      ]
    },
    {
      "page": "count_kmers",
      "title": "K-mer Counting",
      "topics": [
        "count_kmers"
      ]
    },
    {
      "page": "count_pattern",
      "title": "Count Pattern",
      "topics": [
        "count_pattern"
      ]
    },
    {
      "page": "dna_to_protein",
      "title": "Translate DNA to Protein",
      "topics": [
        "dna_to_protein"
      ]
    },
    {
      "page": "dna_to_rna",
      "title": "DNA to RNA",
      "topics": [
        "dna_to_rna"
      ]
    },
    {
      "page": "fastq_to_fasta",
      "title": "Convert FASTQ to FASTA",
      "topics": [
        "fastq_to_fasta"
      ]
    },
    {
      "page": "filter_fastq_quality",
      "title": "Quality Filter FASTQ",
      "topics": [
        "filter_fastq_quality"
      ]
    },
    {
      "page": "find_cpg_islands",
      "title": "CpG Island Detection",
      "topics": [
        "find_cpg_islands"
      ]
    },
    {
      "page": "find_longest_orf",
      "title": "Find Longest ORF",
      "topics": [
        "find_longest_orf"
      ]
    },
    {
      "page": "gc_content",
      "title": "GC Content",
      "topics": [
        "gc_content"
      ]
    },
    {
      "page": "get_genetic_code",
      "title": "Get Genetic Code",
      "topics": [
        "get_genetic_code"
      ]
    },
    {
      "page": "plot_aa_composition",
      "title": "Plot AA Composition",
      "topics": [
        "plot_aa_composition"
      ]
    },
    {
      "page": "plot_dotplot",
      "title": "Plot Dot Plot",
      "topics": [
        "plot_dotplot"
      ]
    },
    {
      "page": "plot_gc_skew",
      "title": "Plot GC Skew",
      "topics": [
        "plot_gc_skew"
      ]
    },
    {
      "page": "plot_hydrophobicity",
      "title": "Plot Hydrophobicity",
      "topics": [
        "plot_hydrophobicity"
      ]
    },
    {
      "page": "read_seq",
      "title": "Universal Sequence Reader",
      "topics": [
        "read_seq"
      ]
    },
    {
      "page": "rev_comp",
      "title": "Universal Reverse Complement",
      "topics": [
        "rev_comp"
      ]
    },
    {
      "page": "reverse_translate",
      "title": "Reverse Translation",
      "topics": [
        "reverse_translate"
      ]
    },
    {
      "page": "rna_to_dna",
      "title": "RNA to DNA",
      "topics": [
        "rna_to_dna"
      ]
    },
    {
      "page": "rna_to_protein",
      "title": "Translate RNA to Protein",
      "topics": [
        "rna_to_protein"
      ]
    },
    {
      "page": "sars_fragment",
      "title": "SARS-CoV-2 Genome Fragment",
      "topics": [
        "sars_fragment"
      ]
    },
    {
      "page": "search_motif",
      "title": "Motif Searching",
      "topics": [
        "search_motif"
      ]
    },
    {
      "page": "shuffle_sequence",
      "title": "Shuffle Sequence",
      "topics": [
        "shuffle_sequence"
      ]
    },
    {
      "page": "simulate_digestion",
      "title": "Virtual Digestion",
      "topics": [
        "simulate_digestion"
      ]
    },
    {
      "page": "simulate_fasta",
      "title": "Simulate FASTA File",
      "topics": [
        "simulate_fasta"
      ]
    },
    {
      "page": "simulate_fastq",
      "title": "Simulate FASTQ File",
      "topics": [
        "simulate_fastq"
      ]
    },
    {
      "page": "simulate_pcr",
      "title": "PCR Simulator",
      "topics": [
        "simulate_pcr"
      ]
    },
    {
      "page": "simulate_sequence",
      "title": "Simulate Sequence",
      "topics": [
        "simulate_sequence"
      ]
    },
    {
      "page": "summarize_fasta",
      "title": "FASTA Summary",
      "topics": [
        "summarize_fasta"
      ]
    },
    {
      "page": "translate",
      "title": "Generic Translate",
      "topics": [
        "translate"
      ]
    },
    {
      "page": "write_seq",
      "title": "Universal Sequence Writer",
      "topics": [
        "write_seq"
      ]
    }
  ],
  "_pkglogo": "https://github.com/ambuvjyn/baseq/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/ambuvjyn/baseq/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "farver",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "baseq-vignette.Rmd",
      "filename": "baseq-vignette.html",
      "title": "Introduction to baseq",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Sequence Cleaning",
        "Translation",
        "GC Content",
        "Reading and Writing Files"
      ],
      "created": "2026-03-11 22:31:52",
      "modified": "2026-03-11 22:31:52",
      "commits": 1
    }
  ],
  "_score": 4.301029995663981,
  "_indexed": true,
  "_nocasepkg": "baseq",
  "_universes": [
    "ambuvjyn"
  ],
  "_progress_url": "https://github.com/r-universe/ambuvjyn/actions/runs/27270236425",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.2.0",
      "date": "2026-05-11T05:47:39.000Z",
      "distro": "noble",
      "commit": "fc12ff769ab08f6467ea4c17b69bdb80a85b198e",
      "fileid": "5b49e5fa3f00f372256550c1d0fb162ba36590d3ff8abf0abb56dfc53d4afbdc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ambuvjyn/actions/runs/25652524480"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.2.0",
      "date": "2026-05-11T05:48:26.000Z",
      "distro": "noble",
      "commit": "fc12ff769ab08f6467ea4c17b69bdb80a85b198e",
      "fileid": "22ca5d9bdf5d4b0380690d9d24d00ce4997f4d02b2644839f2631eba537db610",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ambuvjyn/actions/runs/25652524480"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.2.0",
      "date": "2026-05-11T05:48:23.000Z",
      "commit": "fc12ff769ab08f6467ea4c17b69bdb80a85b198e",
      "fileid": "4d24936a5effba703d4472f47ef84d5358a01db710aa66e25769716e3ba7066f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ambuvjyn/actions/runs/25652524480"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.2.0",
      "date": "2026-05-11T05:47:31.000Z",
      "commit": "fc12ff769ab08f6467ea4c17b69bdb80a85b198e",
      "fileid": "3059769f497dc189f09ccabb37db7d937fe31672d414efbfb08046c72dd705a7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ambuvjyn/actions/runs/25652524480"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.2.0",
      "date": "2026-05-11T05:47:06.000Z",
      "commit": "fc12ff769ab08f6467ea4c17b69bdb80a85b198e",
      "fileid": "71b5ed267902c37591f9a6d5163fde9921552d6ed43626e61e9fbd04795cddd4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ambuvjyn/actions/runs/25652524480"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.2.0",
      "date": "2026-05-11T05:46:57.000Z",
      "commit": "fc12ff769ab08f6467ea4c17b69bdb80a85b198e",
      "fileid": "0791d1d514fe53aebd122d2e8687c72da6df0e094e1c6888217faaebcd3ad8fe",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ambuvjyn/actions/runs/25652524480"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.2.0",
      "date": "2026-05-11T05:47:20.000Z",
      "commit": "fc12ff769ab08f6467ea4c17b69bdb80a85b198e",
      "fileid": "faf92cd0ad265b21279a30f92a5cbec3f6b6bcd0f3f24e129614915247a31ef8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ambuvjyn/actions/runs/25652524480"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.2.0",
      "date": "2026-05-22T12:02:27.000Z",
      "commit": "fc12ff769ab08f6467ea4c17b69bdb80a85b198e",
      "fileid": "4fc0d55ab00175b3a46e8823ada70de515f22b559704904ad23cde7cad59460a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/ambuvjyn/actions/runs/25652524480"
    }
  ]
}