{
  "_id": "6aca451bfe5cc25786e8648b",
  "Package": "methFuse",
  "Title": "Functional Segmentation of the Methylome",
  "Version": "1.1.0",
  "Authors@R": "c(\nperson(\"Susanna\", \"Holmström\", email = \"susanna.k.holmstrom@helsinki.fi\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0009-0005-7542-5913\")),\nperson(\"Antti\", \"Hakkinen\", role = c(\"ctb\", \"cph\")))",
  "Description": "Implements FUSE (Functional Segmentation of DNA\nmethylation data), a data-driven method for identifying\nspatially coherent DNA methylation segments from whole-genome\nbisulfite sequencing (WGBS) count data. The method performs\nhierarchical clustering of CpG sites based on methylated and\nunmethylated read counts across multiple samples and determines\nthe optimal number of segments using an information criterion\n(AIC or BIC). Resulting segments represent regions with\nhomogeneous methylation profiles across the input cohort while\nallowing sample-specific methylation levels. The package\nprovides functions for clustering, model selection, tree\ncutting, segment-level summarization, and visualization. Input\ncan be supplied as count matrices or extracted directly from\n'BSseq' and 'methrix' objects.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "URL": "https://holmsusa.github.io/methFuse/",
  "Repository": "https://holmsusa.r-universe.dev",
  "Date/Publication": "2026-08-03 10:40:40 UTC",
  "RemoteUrl": "https://github.com/holmsusa/methfuse",
  "RemoteRef": "HEAD",
  "RemoteSha": "01600cf9e322f22a79291dae05389daefa90c7ab",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-10 13:53:42 UTC",
    "User": "root"
  },
  "Author": "Susanna Holmström [aut, cre] (ORCID:\n<https://orcid.org/0009-0005-7542-5913>),\nAntti Hakkinen [ctb, cph]",
  "Maintainer": "Susanna Holmström <susanna.k.holmstrom@helsinki.fi>",
  "_user": "holmsusa",
  "_type": "src",
  "_file": "methFuse_1.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/c9719c0c6ab60bff8c5a67e3e3f5d4c088d0e18b80a204199c378895f6c839b3",
  "_filesize": 4577453,
  "_sha256": "c9719c0c6ab60bff8c5a67e3e3f5d4c088d0e18b80a204199c378895f6c839b3",
  "_expires": "2027-01-18T14:00:57.000Z",
  "_created": "2026-10-10T13:53:42.000Z",
  "_published": "2026-10-10T14:00:59.561Z",
  "_buildurl": "https://github.com/r-universe/holmsusa/actions/runs/38057227135",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 114228867013,
      "time": 144,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11672083637"
    },
    {
      "job": 114228867096,
      "time": 176,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11671739079"
    },
    {
      "job": 114228867095,
      "time": 132,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11671714036"
    },
    {
      "job": 114228867017,
      "time": 166,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11671968721"
    },
    {
      "job": 114228867084,
      "time": 238,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11671824189"
    },
    {
      "job": 114228867107,
      "time": 270,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11671959073"
    },
    {
      "job": 114228867101,
      "time": 185,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11671282883"
    },
    {
      "job": 114228867030,
      "time": 357,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11671424541"
    },
    {
      "job": 114228127294,
      "time": 236,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11672083346"
    },
    {
      "job": 114228867047,
      "time": 128,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11671803794"
    },
    {
      "job": 114228867086,
      "time": 365,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11671584331"
    },
    {
      "job": 114228867093,
      "time": 170,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11671853903"
    },
    {
      "job": 114228867098,
      "time": 121,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11672128352"
    },
    {
      "job": 114228867049,
      "time": 348,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11671427869"
    },
    {
      "job": 114228867055,
      "time": 128,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11671024512"
    }
  ],
  "_upstream": "https://github.com/holmsusa/methfuse",
  "_commit": {
    "id": "01600cf9e322f22a79291dae05389daefa90c7ab",
    "author": "holmsusa <127730085+holmsusa@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Update README with publication link\n\nAdded a link to the publication for further details.",
    "time": 1785753640
  },
  "_maintainer": {
    "name": "Susanna Holmström",
    "email": "susanna.k.holmstrom@helsinki.fi",
    "login": "holmsusa",
    "description": "",
    "uuid": 127730085,
    "orcid": "0009-0005-7542-5913"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "bsseq",
      "role": "Suggests"
    },
    {
      "package": "methrix",
      "role": "Suggests"
    },
    {
      "package": "beachmat",
      "role": "Suggests"
    },
    {
      "package": "GenomicRanges",
      "role": "Suggests"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Suggests"
    },
    {
      "package": "DelayedArray",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "graphics",
      "role": "Suggests"
    }
  ],
  "_owner": "holmsusa",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-41",
      "n": 2
    },
    {
      "week": "2025-42",
      "n": 5
    },
    {
      "week": "2025-46",
      "n": 1
    },
    {
      "week": "2025-47",
      "n": 12
    },
    {
      "week": "2025-48",
      "n": 8
    },
    {
      "week": "2025-51",
      "n": 1
    },
    {
      "week": "2026-06",
      "n": 7
    },
    {
      "week": "2026-07",
      "n": 1
    },
    {
      "week": "2026-08",
      "n": 7
    },
    {
      "week": "2026-09",
      "n": 1
    },
    {
      "week": "2026-32",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "v1.0.0",
      "date": "2026-02-12"
    },
    {
      "name": "v1.1.0",
      "date": "2026-02-12"
    }
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "holmsusa",
      "count": 84,
      "uuid": 127730085
    }
  ],
  "_userbio": {
    "uuid": 127730085,
    "type": "user",
    "name": "holmsusa",
    "followers": 3
  },
  "_downloads": {
    "count": 326,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/methFuse"
  },
  "_devurl": "https://github.com/holmsusa/methfuse",
  "_pkgdown": "https://holmsusa.github.io/methFuse/",
  "_searchresults": 3,
  "_topics": [
    "openmp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/methFuse.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/holmsusa/methfuse",
  "_realowner": "holmsusa",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.1.0",
      "date": "2026-03-04"
    }
  ],
  "_exports": [
    "fuse.cluster",
    "fuse.cut.tree",
    "fuse.segment",
    "fuse.summary",
    "number.of.clusters"
  ],
  "_help": [
    {
      "page": "fuse.cluster",
      "title": "Perform Hierarchical Clustering on Methylation Data",
      "topics": [
        "fuse.cluster",
        "fuse.cluster.BSseq",
        "fuse.cluster.default",
        "fuse.cluster.methrix"
      ]
    },
    {
      "page": "fuse.cut.tree",
      "title": "Cut Hierarchical Clustering Tree into Clusters",
      "topics": [
        "fuse.cut.tree"
      ]
    },
    {
      "page": "fuse.segment",
      "title": "Full FUSE segmentation pipeline",
      "topics": [
        "fuse.segment",
        "fuse.segment.BSseq",
        "fuse.segment.default",
        "fuse.segment.methrix"
      ]
    },
    {
      "page": "fuse.summary",
      "title": "Summarize FUSE Segmentation Results",
      "topics": [
        "fuse.summary"
      ]
    },
    {
      "page": "number.of.clusters",
      "title": "Find Optimal Number of Clusters",
      "topics": [
        "number.of.clusters"
      ]
    },
    {
      "page": "plot.fuse_summary",
      "title": "Plot method for FUSE segmentation results",
      "topics": [
        "plot.fuse_summary"
      ]
    }
  ],
  "_readme": "https://github.com/holmsusa/methfuse/raw/HEAD/README.md",
  "_rundeps": [],
  "_sysdeps": [
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_vignettes": [
    {
      "source": "example.Rmd",
      "filename": "example.html",
      "title": "Example workflow using FUSE",
      "author": "Susanna Holmstrom",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Reading in data",
        "Apply FUSE as a pipeline",
        "Using BSseq or methrix",
        "Apply FUSE through separate steps",
        "1. Cluster",
        "2. Cutting the tree",
        "3. Summarizing segments",
        "Verification",
        "Plotting"
      ],
      "created": "2025-11-20 12:58:46",
      "modified": "2026-02-27 14:43:19",
      "commits": 13
    }
  ],
  "_score": 5.041392685158225,
  "_indexed": true,
  "_nocasepkg": "methfuse",
  "_universes": [
    "holmsusa"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-10-10T13:55:51.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "01600cf9e322f22a79291dae05389daefa90c7ab",
      "fileid": "https://r2.ropensci.org/b82ae5bdf4a2d37c8af8b263f7a0914a8cc87c3d35b90d43fbe87f880e345dc3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/holmsusa/actions/runs/38057227135"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-10-10T13:56:09.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "01600cf9e322f22a79291dae05389daefa90c7ab",
      "fileid": "https://r2.ropensci.org/c7f89cd900923770d98899809daa38b868d1a6403f86856c1ab2a2d04b0128f7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/holmsusa/actions/runs/38057227135"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-10-10T13:55:45.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "01600cf9e322f22a79291dae05389daefa90c7ab",
      "fileid": "https://r2.ropensci.org/a1ec01a9fae48ba4b90379a57b971bcd617267f8938333c030729b94d7a636cf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/holmsusa/actions/runs/38057227135"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-10-10T13:56:05.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "01600cf9e322f22a79291dae05389daefa90c7ab",
      "fileid": "https://r2.ropensci.org/a514fb4f41ff65232a9c68f2324dc349960963c5241c9356de2b925cbfae83ca",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/holmsusa/actions/runs/38057227135"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-10-10T13:57:56.000Z",
      "arch": "aarch64",
      "commit": "01600cf9e322f22a79291dae05389daefa90c7ab",
      "fileid": "https://r2.ropensci.org/0e09331436cdc975eeb06cd36deef4eeb2edcd9d13b20d8eac15dde3ceee5864",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/holmsusa/actions/runs/38057227135"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-10-10T13:57:31.000Z",
      "arch": "x86_64",
      "commit": "01600cf9e322f22a79291dae05389daefa90c7ab",
      "fileid": "https://r2.ropensci.org/80f21364d4c53a71a4891db9343d9c9bccd6ab588d8462b88fb550814668528b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/holmsusa/actions/runs/38057227135"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-10-10T13:57:18.000Z",
      "arch": "aarch64",
      "commit": "01600cf9e322f22a79291dae05389daefa90c7ab",
      "fileid": "https://r2.ropensci.org/7a97b0e51502c8c43868976d2050309e18d2a108da6be9658f966cca1f452924",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/holmsusa/actions/runs/38057227135"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-10-10T13:58:40.000Z",
      "arch": "x86_64",
      "commit": "01600cf9e322f22a79291dae05389daefa90c7ab",
      "fileid": "https://r2.ropensci.org/20720ed6849953653af47d2a1a6952b877e8e070ebfdff1a8758d8efcfaa82af",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/holmsusa/actions/runs/38057227135"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.0",
      "date": "2026-10-10T13:56:04.000Z",
      "arch": "emscripten",
      "commit": "01600cf9e322f22a79291dae05389daefa90c7ab",
      "fileid": "https://r2.ropensci.org/8bf1f1e420a090858469733389a0c2f3a7dfba899a7ed615f7fee1073c58472e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/holmsusa/actions/runs/38057227135"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-10-10T13:58:51.000Z",
      "arch": "aarch64",
      "commit": "01600cf9e322f22a79291dae05389daefa90c7ab",
      "fileid": "https://r2.ropensci.org/9fdf274eacb7821617ad6de7af9ef726a7ff2fff7ca2661c3b8309d0185042f0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/holmsusa/actions/runs/38057227135"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-10-10T13:55:17.000Z",
      "arch": "x86_64",
      "commit": "01600cf9e322f22a79291dae05389daefa90c7ab",
      "fileid": "https://r2.ropensci.org/db159dca2b331c4935238a86277f375ea132d6bd2e4c845f4cf49f9cc3ec5c7e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/holmsusa/actions/runs/38057227135"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-10-10T13:55:07.000Z",
      "arch": "x86_64",
      "commit": "01600cf9e322f22a79291dae05389daefa90c7ab",
      "fileid": "https://r2.ropensci.org/d0c244dcee045b1915220ae4440930ea367f579d75ed4e59c1ef65e9bd12ece3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/holmsusa/actions/runs/38057227135"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-10-10T13:58:28.000Z",
      "arch": "aarch64",
      "commit": "01600cf9e322f22a79291dae05389daefa90c7ab",
      "fileid": "https://r2.ropensci.org/3227f62c08b1b36ea84eaa78a4b9dcfbf99185fd95c20cb59fa76819d6172de6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/holmsusa/actions/runs/38057227135"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-10-10T13:55:15.000Z",
      "arch": "x86_64",
      "commit": "01600cf9e322f22a79291dae05389daefa90c7ab",
      "fileid": "https://r2.ropensci.org/6932f6a7296b99cc31db7a8e625f410b83f125121f50d36d72976dcaf50d3f9a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/holmsusa/actions/runs/38057227135"
    }
  ]
}