{
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  "Package": "seqmagick",
  "Title": "Sequence Manipulation Utilities",
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  "Authors@R": "c(\nperson(\"Guangchuang\", \"Yu\",     email = \"guangchuangyu@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6485-8781\"))\n)",
  "Description": "Tools for reading and writing biological sequences in\nmultiple formats, including 'FASTA', 'PHYLIP', 'CLUSTAL',\n'STOCKHOLM', 'MEGA' and 'GenBank'. Supports interleaved and\nsequential layouts where applicable, converts between formats,\nand manipulates sequence sets (e.g., filtering by patterns and\ncomputing consensus sequences from alignments). Also includes\nfunctions to download nucleotide records from NCBI by\naccession.",
  "VignetteBuilder": "knitr",
  "ByteCompile": "true",
  "URL": "https://github.com/YuLab-SMU/seqmagick",
  "BugReports": "https://github.com/YuLab-SMU/seqmagick/issues",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "cmake make libuv1-dev zlib1g-dev",
  "Repository": "https://yulab-smu.r-universe.dev",
  "Date/Publication": "2026-01-31 07:39:40 UTC",
  "RemoteUrl": "https://github.com/yulab-smu/seqmagick",
  "RemoteRef": "HEAD",
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    "User": "root"
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  "Author": "Guangchuang Yu [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-6485-8781>)",
  "Maintainer": "Guangchuang Yu <guangchuangyu@gmail.com>",
  "MD5sum": "dfa86dc82512d0bcdcdfa21dd571b56a",
  "_user": "yulab-smu",
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    "author": "Guangchuang Yu <guangchuangyu@gmail.com>",
    "committer": "Guangchuang Yu <guangchuangyu@gmail.com>",
    "message": "use yulab.utils:::mydownload\n",
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    "name": "Guangchuang Yu",
    "email": "guangchuangyu@gmail.com",
    "login": "guangchuangyu",
    "twitter": "@guangchuangyu",
    "uuid": 626539,
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      "role": "Imports"
    },
    {
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      "role": "Imports"
    },
    {
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      "role": "Suggests"
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    {
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    {
      "package": "GenomicRanges",
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    },
    {
      "package": "IRanges",
      "role": "Suggests"
    },
    {
      "package": "muscle",
      "role": "Suggests"
    },
    {
      "package": "Rsamtools",
      "role": "Suggests"
    },
    {
      "package": "prettydoc",
      "role": "Suggests"
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  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
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      "week": "2026-05",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 6,
  "_contributors": [
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      "count": 47,
      "uuid": 626539
    },
    {
      "user": "xiangpin",
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      "uuid": 17870644
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  ],
  "_userbio": {
    "uuid": 40430016,
    "type": "organization",
    "name": "Bioinformatics Group @ SMU",
    "description": "Research group led by Prof. Guangchuang Yu in School of Basic Medical Sciences, Southern Medical University"
  },
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    "count": 1246,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/seqmagick"
  },
  "_devurl": "https://github.com/yulab-smu/seqmagick",
  "_searchresults": 13,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/seqmagick.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/yulab-smu/seqmagick",
  "_realowner": "yulab-smu",
  "_cranurl": true,
  "_releases": [
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      "version": "0.1.1",
      "date": "2019-12-17"
    },
    {
      "version": "0.1.2",
      "date": "2019-12-18"
    },
    {
      "version": "0.1.3",
      "date": "2019-12-19"
    },
    {
      "version": "0.1.4",
      "date": "2020-09-22"
    },
    {
      "version": "0.1.5",
      "date": "2021-04-25"
    },
    {
      "version": "0.1.6",
      "date": "2023-06-27"
    },
    {
      "version": "0.1.7",
      "date": "2024-01-09"
    },
    {
      "version": "0.1.8",
      "date": "2026-01-31"
    }
  ],
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    "bam2DNAStringSet",
    "bam2DNAStringSet2",
    "bs_aln",
    "bs_consensus",
    "bs_filter",
    "bs_hamming",
    "bs_rename",
    "clw_read",
    "consensus",
    "download_genbank",
    "fa_combine",
    "fa_filter",
    "fa_read",
    "fa_rename",
    "fa_to_interleaved",
    "fa_to_sequential",
    "fa_write",
    "fas2phy",
    "gb_read",
    "get_id",
    "mega_read",
    "ncbi_fa_read",
    "phy_read",
    "phy_write",
    "phy2fas",
    "renameTXT",
    "replaceInside",
    "seqlen",
    "sth_read"
  ],
  "_help": [
    {
      "page": "bam2DNAStringSet",
      "title": "bam2DNAStringSet",
      "topics": [
        "bam2DNAStringSet"
      ]
    },
    {
      "page": "bam2DNAStringSet2",
      "title": "bam2DNAStringSet2",
      "topics": [
        "bam2DNAStringSet2"
      ]
    },
    {
      "page": "bs_aln",
      "title": "bs_aln",
      "topics": [
        "bs_aln"
      ]
    },
    {
      "page": "bs_filter",
      "title": "bs_filter",
      "topics": [
        "bs_filter"
      ]
    },
    {
      "page": "bs_hamming",
      "title": "bs_hamming",
      "topics": [
        "bs_hamming"
      ]
    },
    {
      "page": "bs_rename",
      "title": "bs_rename",
      "topics": [
        "bs_rename"
      ]
    },
    {
      "page": "consensus",
      "title": "consensus",
      "topics": [
        "bs_consensus",
        "consensus"
      ]
    },
    {
      "page": "download_genbank",
      "title": "download_genbank",
      "topics": [
        "download_genbank"
      ]
    },
    {
      "page": "fa_combine",
      "title": "fa_combine",
      "topics": [
        "fa_combine"
      ]
    },
    {
      "page": "fa_filter",
      "title": "fa_filter",
      "topics": [
        "fa_filter"
      ]
    },
    {
      "page": "fa_rename",
      "title": "fa_rename",
      "topics": [
        "fa_rename"
      ]
    },
    {
      "page": "fa_conversion",
      "title": "fa_to_interleaved",
      "topics": [
        "fa_to_interleaved",
        "fa_to_sequential"
      ]
    },
    {
      "page": "fa_write",
      "title": "fa_write",
      "topics": [
        "fa_write"
      ]
    },
    {
      "page": "fas2phy",
      "title": "fas2phy",
      "topics": [
        "fas2phy"
      ]
    },
    {
      "page": "gb_read",
      "title": "gb_read",
      "topics": [
        "gb_read"
      ]
    },
    {
      "page": "get_id",
      "title": "get_id",
      "topics": [
        "get_id"
      ]
    },
    {
      "page": "msa-read",
      "title": "read sequence alignment file",
      "topics": [
        "clw_read",
        "fa_read",
        "mega_read",
        "sth_read"
      ]
    },
    {
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      "title": "ncbi_fa_read",
      "topics": [
        "ncbi_fa_read"
      ]
    },
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      "page": "phy_read",
      "title": "phy_read",
      "topics": [
        "phy_read"
      ]
    },
    {
      "page": "phy_write",
      "title": "phy_write",
      "topics": [
        "phy_write"
      ]
    },
    {
      "page": "phy2fas",
      "title": "phy2fas",
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        "phy2fas"
      ]
    },
    {
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      "title": "renameTXT",
      "topics": [
        "renameTXT"
      ]
    },
    {
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      "title": "replaceInside",
      "topics": [
        "replaceInside"
      ]
    },
    {
      "page": "seqlen",
      "title": "seqlen",
      "topics": [
        "seqlen"
      ]
    }
  ],
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    "Biostrings",
    "cli",
    "crayon",
    "digest",
    "fs",
    "generics",
    "IRanges",
    "magrittr",
    "rappdirs",
    "rlang",
    "S4Vectors",
    "Seqinfo",
    "XVector",
    "yulab.utils"
  ],
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      "source": "seqmagick.Rmd",
      "filename": "seqmagick.html",
      "title": "seqmagick: sequence manipulation",
      "author": "Guangchuang Yu",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "Genbank",
        "File conversion",
        "fasta and phylip conversion",
        "interleaved and sequential format conversion",
        "Sequence manipulation",
        "Bugs/Feature requests",
        "Session info",
        "References"
      ],
      "created": "2016-06-20 11:02:22",
      "modified": "2020-09-22 07:08:50",
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