{
  "_id": "6a62eef4d3420cf5dfdb4c55",
  "Package": "mire",
  "Title": "Microbiome Integrated Reconstruction and Estimation",
  "Version": "0.0.1.9000",
  "Authors@R": "person(\"Yun\", \"Peng\", , \"pengyun.me@outlook.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-2801-3332\"))",
  "Description": "An integrated framework for microbiome reconstruction from\nsequencing data. It leverages tools like Kraken2 for taxonomic\nclassification and combines cell barcodes, UMIs, and\nk-mer-based quantification to reconstruct microbial signals.\nDesigned for both bulk and single-cell sequencing data, the\npackage enables taxonomic and quantitative profiling of\nmicrobial communities.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/WangLabCSU/mire",
  "BugReports": "https://github.com/WangLabCSU/mire/issues",
  "ByteCompile": "true",
  "Encoding": "UTF-8",
  "Config/build/copy-method": "link",
  "Config/roxygen2/version": "8.0.0",
  "Roxygen": "list(markdown = TRUE)",
  "SystemRequirements": "Cargo (Rust's package manager), rustc, kraken2",
  "Config/pak/sysreqs": "libclang-dev",
  "Repository": "https://wanglabcsu.r-universe.dev",
  "Date/Publication": "2026-07-23 10:35:44 UTC",
  "RemoteUrl": "https://github.com/WangLabCSU/mire",
  "RemoteRef": "HEAD",
  "RemoteSha": "dd6dbe60186721ffd51c396609f651195cfc5485",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-23 11:04:30 UTC",
    "User": "root"
  },
  "Author": "Yun Peng [aut, cre] (ORCID: <https://orcid.org/0000-0003-2801-3332>)",
  "Maintainer": "Yun Peng <pengyun.me@outlook.com>",
  "_user": "wanglabcsu",
  "_type": "src",
  "_file": "mire_0.0.1.9000.tar.gz",
  "_fileid": "https://r2.ropensci.org/b605e5cef152065afacbf84920aa0d56ac63f1c1976019353ef76752535f4c68",
  "_filesize": 4811714,
  "_sha256": "b605e5cef152065afacbf84920aa0d56ac63f1c1976019353ef76752535f4c68",
  "_expires": "2026-10-31T11:16:56.000Z",
  "_created": "2026-07-23T11:04:30.000Z",
  "_published": "2026-07-24T04:49:56.894Z",
  "_jobs": [
    {
      "job": 89401684577,
      "time": 191,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8561358520"
    },
    {
      "job": 89401684475,
      "time": 174,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8561352520"
    },
    {
      "job": 89401684662,
      "time": 161,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8561346739"
    },
    {
      "job": 89401684797,
      "time": 180,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8561354415"
    },
    {
      "job": 89401684798,
      "time": 142,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8561441087"
    },
    {
      "job": 89401684731,
      "time": 345,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8561511321"
    },
    {
      "job": 89401684481,
      "time": 130,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8561441919"
    },
    {
      "job": 89401684646,
      "time": 296,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8561569218"
    },
    {
      "job": 89401684424,
      "time": 186,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8561271894"
    },
    {
      "job": 89401684118,
      "time": 115,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 89401684146,
      "time": 153,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 89401684151,
      "time": 179,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 89401684150,
      "time": 166,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "FAIL",
      "artifact": ""
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/wanglabcsu/actions/runs/30001568702",
  "_status": "success",
  "_upstream": "https://github.com/WangLabCSU/mire",
  "_commit": {
    "id": "dd6dbe60186721ffd51c396609f651195cfc5485",
    "author": "Yunuuuu <pengyun.me@outlook.com>",
    "committer": "Yunuuuu <pengyun.me@outlook.com>",
    "message": "refactor: unset classified_out by default\n",
    "time": 1784802944
  },
  "_maintainer": {
    "name": "Yun Peng",
    "email": "pengyun.me@outlook.com",
    "login": "yunuuuu",
    "orcid": "0000-0003-2801-3332",
    "description": "",
    "uuid": 19575010
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2",
      "role": "Depends"
    },
    {
      "package": "mirai",
      "role": "Imports"
    },
    {
      "package": "cli",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    }
  ],
  "_owner": "wanglabcsu",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-33",
      "n": 1
    },
    {
      "week": "2026-30",
      "n": 7
    }
  ],
  "_tags": [],
  "_stars": 4,
  "_contributors": [
    {
      "user": "yunuuuu",
      "count": 7,
      "uuid": 19575010
    }
  ],
  "_userbio": {
    "uuid": 177597689,
    "type": "organization",
    "name": "Laboratory of *In Silico* Oncology and Medicine (LISOM)",
    "followers": 33,
    "description": "Dr. Shixiang Wang' lab at Central South University"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/mire"
  },
  "_devurl": "https://github.com/wanglabcsu/mire",
  "_searchresults": 3,
  "_cargo": true,
  "_topics": [
    "rust",
    "cargo"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/mire.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "blsd",
    "denoise_counts",
    "embed",
    "embed_trim",
    "koutreads",
    "kractor_koutput",
    "kractor_reads",
    "kraken2",
    "krcount",
    "read_kreport",
    "rpmm_quantile",
    "seq_range",
    "seq_refine",
    "slsd",
    "tag",
    "trim"
  ],
  "_help": [
    {
      "page": "blsd",
      "title": "Barcode level signal denoising",
      "topics": [
        "blsd"
      ]
    },
    {
      "page": "denoise_counts",
      "title": "Denoise and Quantify Taxa from Kraken2 Results",
      "topics": [
        "denoise_counts"
      ]
    },
    {
      "page": "koutreads",
      "title": "Kraken2 Output Processing for FASTQ Files",
      "topics": [
        "koutreads",
        "tag"
      ]
    },
    {
      "page": "kractor_koutput",
      "title": "Filter Kraken2 Output by Taxon",
      "topics": [
        "kractor_koutput"
      ]
    },
    {
      "page": "kractor_reads",
      "title": "Extract Reads from Kraken2 Output Based on Classification",
      "topics": [
        "kractor_reads"
      ]
    },
    {
      "page": "kraken2",
      "title": "Run Kraken2 for Taxonomic Classification",
      "topics": [
        "kraken2"
      ]
    },
    {
      "page": "krcount",
      "title": "Quantify K-mers and UMI Data by Taxon",
      "topics": [
        "krcount"
      ]
    },
    {
      "page": "read_kreport",
      "title": "Parse kraken report file",
      "topics": [
        "read_kreport"
      ]
    },
    {
      "page": "rpmm_quantile",
      "title": "Identifying contaminants and false positives taxa (cell line quantile test)",
      "topics": [
        "rpmm_quantile"
      ]
    },
    {
      "page": "seq_range",
      "title": "Create a UMI/Barcode range",
      "topics": [
        "seq_range"
      ]
    },
    {
      "page": "seq_refine",
      "title": "Refine Sequences from FASTQ Files with UMI/Barcode Actions",
      "topics": [
        "seq_refine"
      ]
    },
    {
      "page": "slsd",
      "title": "Sample level signal denoising",
      "topics": [
        "slsd"
      ]
    },
    {
      "page": "subseq_actions",
      "title": "Define sequence range behavior: embed, trim, or both",
      "topics": [
        "embed",
        "embed_trim",
        "subseq_actions",
        "trim"
      ]
    }
  ],
  "_readme": "https://github.com/WangLabCSU/mire/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "farver",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "mirai",
    "nanonext",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_score": 2.6020599913279625,
  "_indexed": true,
  "_nocasepkg": "mire",
  "_universes": [
    "wanglabcsu",
    "yunuuuu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.0.1.9000",
      "date": "2026-07-12T09:05:56.000Z",
      "arch": "x86_64",
      "commit": "566070a04b4776049e03e79e1b6d516a98b0c38f",
      "fileid": "https://r2.ropensci.org/e80a75eadcb37b7f288ae4cc5057616c4d1f8478921ff4036ebd3422b7d937fe",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/wanglabcsu/actions/runs/29186757296"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.0.1.9000",
      "date": "2026-07-12T09:06:31.000Z",
      "arch": "x86_64",
      "commit": "566070a04b4776049e03e79e1b6d516a98b0c38f",
      "fileid": "https://r2.ropensci.org/406fe5f9c6f142cf16858262dcb584082449ecac7173629f9c57ac873fc87f1b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/wanglabcsu/actions/runs/29186757296"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.0.1.9000",
      "date": "2026-07-12T09:05:53.000Z",
      "arch": "x86_64",
      "commit": "566070a04b4776049e03e79e1b6d516a98b0c38f",
      "fileid": "https://r2.ropensci.org/c69ea3af5cd5981babe025435bdbc7361d9b0a047a7941c31d8e84069647a698",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/wanglabcsu/actions/runs/29186757296"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.0.1.9000",
      "date": "2026-07-23T11:07:39.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "dd6dbe60186721ffd51c396609f651195cfc5485",
      "fileid": "https://r2.ropensci.org/afafcd8db2563625d88b4c551d6d4ff1badb264ce97aa02241418587855fd77a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/wanglabcsu/actions/runs/30001568702"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.0.1.9000",
      "date": "2026-07-23T11:07:16.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "dd6dbe60186721ffd51c396609f651195cfc5485",
      "fileid": "https://r2.ropensci.org/90bd23f29af9fd125b35b60108539d7103855ed26da82bc7f5ca2df72145a58e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/wanglabcsu/actions/runs/30001568702"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.0.1.9000",
      "date": "2026-07-23T11:07:12.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "dd6dbe60186721ffd51c396609f651195cfc5485",
      "fileid": "https://r2.ropensci.org/07e76ce5e54a44ccee1b72ca3dd6c86124113590738bcd365afd83b81b03d1a1",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/wanglabcsu/actions/runs/30001568702"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.0.1.9000",
      "date": "2026-07-23T11:07:23.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "dd6dbe60186721ffd51c396609f651195cfc5485",
      "fileid": "https://r2.ropensci.org/c76f363e44fe05c08f21821a59a4d69f66018c449023b558ae6fbd8e416a7fae",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/wanglabcsu/actions/runs/30001568702"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.0.1.9000",
      "date": "2026-07-23T11:10:44.000Z",
      "arch": "aarch64",
      "commit": "dd6dbe60186721ffd51c396609f651195cfc5485",
      "fileid": "https://r2.ropensci.org/c1332425e6cdc71d320f57f00d5423f49b817406b6337eadf7d44e0173ebcfc0",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/wanglabcsu/actions/runs/30001568702"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.0.1.9000",
      "date": "2026-07-23T11:12:02.000Z",
      "arch": "x86_64",
      "commit": "dd6dbe60186721ffd51c396609f651195cfc5485",
      "fileid": "https://r2.ropensci.org/cda2afdeb867e16a8f90525af204c67a4b2e00af04d343ad9bff45b4a6373c00",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/wanglabcsu/actions/runs/30001568702"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.0.1.9000",
      "date": "2026-07-23T11:10:49.000Z",
      "arch": "aarch64",
      "commit": "dd6dbe60186721ffd51c396609f651195cfc5485",
      "fileid": "https://r2.ropensci.org/fe5776b4fc8ece61336181e56a44bf2088ed6ef4dcdf65502f3e627250bc7320",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/wanglabcsu/actions/runs/30001568702"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.0.1.9000",
      "date": "2026-07-23T11:14:31.000Z",
      "arch": "x86_64",
      "commit": "dd6dbe60186721ffd51c396609f651195cfc5485",
      "fileid": "https://r2.ropensci.org/6050905e9e62114349de381db1e54abdfd642531afe1b788e6e909d5ba82076f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/wanglabcsu/actions/runs/30001568702"
    }
  ]
}