{ "_id": "6addeacfeef27ed744a9f9d7", "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", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "URL": "https://holmsusa.github.io/methFuse/", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-25 11:36:08 UTC", "User": "root" }, "Author": "Susanna Holmström [aut, cre] (ORCID:\n), Antti Hakkinen [ctb,\ncph]", "Maintainer": "Susanna Holmström ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-03-04 10:10:02 UTC", "RemoteUrl": "https://github.com/cran/methFuse", "RemoteRef": "HEAD", "RemoteSha": "36ab1c58aea1c071427501357886e99ecd2fac23", "_user": "cran", "_type": "src", "_file": "methFuse_1.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/c9c15a165d19804b8095aa4f088d89d80157fc8bce7c5900ce8fad2ed49d8e42", "_filesize": 4578916, "_sha256": "c9c15a165d19804b8095aa4f088d89d80157fc8bce7c5900ce8fad2ed49d8e42", "_expires": "2027-02-02T11:41:01.000Z", "_created": "2026-10-25T11:36:08.000Z", "_published": "2026-10-25T11:41:02.928Z", "_upstream": "https://github.com/cran/methFuse", "_status": "success", "_maintainer": { "name": "Susanna Holmström", "email": "susanna.k.holmstrom@helsinki.fi", "login": "holmsusa", "description": "", "uuid": 127730085, "orcid": "0009-0005-7542-5913" }, "_jobs": [ { "job": 121157503289, "time": 143, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12596513880" }, { "job": 121157503151, "time": 197, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12597194745" }, { "job": 121157503155, "time": 135, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12597259425" }, { "job": 121157503120, "time": 184, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12596513924" }, { "job": 121156669148, "time": 237, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12596718286" }, { "job": 121157503105, "time": 128, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12596493949" }, { "job": 121157503168, "time": 233, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12597559010" }, { "job": 121157503218, "time": 183, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12597094705" }, { "job": 121157503181, "time": 256, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12597735166" }, { "job": 121157503156, "time": 128, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12597474024" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/40189272596", "_commit": { "id": "36ab1c58aea1c071427501357886e99ecd2fac23", "author": "Susanna Holmström ", "committer": "cran-robot ", "message": "version 1.1.0\n", "time": 1772619002 }, "_distro": "resolute", "_host": "GitHub-Actions", "_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": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-10", "n": 1 } ], "_tags": [ { "name": "1.1.0", "date": "2026-03-04" } ], "_stars": 0, "_contributors": [ { "user": "holmsusa", "count": 1, "uuid": 127730085 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 634, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 285, "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": false, "_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/cran/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": "2026-03-04 10:10:02", "modified": "2026-03-04 10:10:02", "commits": 1 } ], "_score": 2.6989700043360187, "_indexed": false, "_nocasepkg": "methfuse", "_universes": [ "cran" ], "_indexurl": "https://holmsusa.r-universe.dev/methFuse", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.0", "date": "2026-10-25T11:38:19.000Z", "distro": "resolute", "arch": "aarch64", "commit": "36ab1c58aea1c071427501357886e99ecd2fac23", "fileid": "https://r2.ropensci.org/d1fe368693cae95922d5e5aa598505b7d210e70cdbf318beb2ea84f832897ad7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40189272596" }, { "r": "4.7.0", "os": "linux", "version": "1.1.0", "date": "2026-10-25T11:39:05.000Z", "distro": "resolute", "arch": "x86_64", "commit": "36ab1c58aea1c071427501357886e99ecd2fac23", "fileid": "https://r2.ropensci.org/a7babcecfdc141f1e8544aa4b581b36486c64c93e8120a26fdc42d0ed11ba203", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40189272596" }, { "r": "4.6.1", "os": "linux", "version": "1.1.0", "date": "2026-10-25T11:38:14.000Z", "distro": "resolute", "arch": "aarch64", "commit": "36ab1c58aea1c071427501357886e99ecd2fac23", "fileid": "https://r2.ropensci.org/f43d735542e8b0a1706c5750e25cdecbe8bce2a1ea8a13cea8d2f89e8a64cb59", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40189272596" }, { "r": "4.6.1", "os": "linux", "version": "1.1.0", "date": "2026-10-25T11:38:46.000Z", "distro": "resolute", "arch": "x86_64", "commit": "36ab1c58aea1c071427501357886e99ecd2fac23", "fileid": "https://r2.ropensci.org/4d374703aa29d3bd40386f08e8763ae24362a9329012587105e06fdd8ce90cb5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40189272596" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.0", "date": "2026-10-25T11:38:34.000Z", "arch": "emscripten", "commit": "36ab1c58aea1c071427501357886e99ecd2fac23", "fileid": "https://r2.ropensci.org/a2106bf317f6609ac80db078b3b107afe308fa11b789cd2d33b03e58bc5affbb", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/40189272596" }, { "r": "4.7.0", "os": "win", "version": "1.1.0", "date": "2026-10-25T11:39:34.000Z", "arch": "aarch64", "commit": "36ab1c58aea1c071427501357886e99ecd2fac23", "fileid": "https://r2.ropensci.org/7d5f054dab98cde42ec5290d5d2ebe819ec00a2321e89af4f9d8bac090182afa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40189272596" }, { "r": "4.7.0", "os": "win", "version": "1.1.0", "date": "2026-10-25T11:38:00.000Z", "arch": "x86_64", "commit": "36ab1c58aea1c071427501357886e99ecd2fac23", "fileid": "https://r2.ropensci.org/c4002f4f466c469a5c1727ee95457dd6104e5a0db798934c6a979a36b9b6e3db", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40189272596" }, { "r": "4.6.1", "os": "win", "version": "1.1.0", "date": "2026-10-25T11:40:01.000Z", "arch": "aarch64", "commit": "36ab1c58aea1c071427501357886e99ecd2fac23", "fileid": "https://r2.ropensci.org/50e9cc5ff40c25e8b96f4226c87af7442907e9d6baf94d7467319682846aabb1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40189272596" }, { "r": "4.6.1", "os": "win", "version": "1.1.0", "date": "2026-10-25T11:37:41.000Z", "arch": "x86_64", "commit": "36ab1c58aea1c071427501357886e99ecd2fac23", "fileid": "https://r2.ropensci.org/0ec380fdb6a4de24e68579fbe007c759fefaccbb730cf960d4c14e1c871c0c8c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40189272596" } ] }