{ "_id": "6a1af8881d7bb097a09fae01", "Package": "smoothclust", "Version": "1.9.1", "Title": "smoothclust", "Description": "Method for identification of spatial domains and\nspatially-aware clustering in spatial transcriptomics data. The\nmethod generates spatial domains with smooth boundaries by\nsmoothing gene expression profiles across neighboring spatial\nlocations, followed by unsupervised clustering. Spatial domains\nconsisting of consistent mixtures of cell types may then be\nfurther investigated by applying cell type compositional\nanalyses or differential analyses.", "Authors@R": "c(\nperson(\"Lukas M.\", \"Weber\",\nemail = \"lmweb012@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-3282-1730\")))", "URL": "https://github.com/lmweber/smoothclust", "BugReports": "https://github.com/lmweber/smoothclust/issues", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "biocViews": "Spatial, SingleCell, Transcriptomics, GeneExpression,\nClustering", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libmagick++-dev gsfonts libicu-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 19:55:46 UTC", "RemoteUrl": "https://github.com/bioc/smoothclust", "RemoteRef": "HEAD", "RemoteSha": "76b863ed5ef27dd6503d036912716f43dfd8c75c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:48:13 UTC", "User": "root" }, "Author": "Lukas M. Weber [aut, cre] (ORCID:\n)", "Maintainer": "Lukas M. Weber ", "MD5sum": "2fa68f4fd5a39728b3a9e3cbb263089c", "_user": "bioc", "_type": "src", "_file": "smoothclust_1.9.1.tar.gz", "_fileid": "67f100f605504570eb542393b2f45475ef62e2106987c05781151868a992d750", "_filesize": 192672, "_sha256": "67f100f605504570eb542393b2f45475ef62e2106987c05781151868a992d750", "_created": "2026-05-30T09:48:13.000Z", "_published": "2026-05-30T14:47:36.446Z", "_jobs": [ { "job": 78640686367, "time": 223, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307509414" }, { "job": 78640686374, "time": 422, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7307526106" }, { "job": 78640686372, "time": 442, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7307527776" }, { "job": 78640686373, "time": 209, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7308978211" }, { "job": 78640686371, "time": 306, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7308989159" }, { "job": 78639894918, "time": 342, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307298314" }, { "job": 78640686368, "time": 192, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307506706" }, { "job": 78640686376, "time": 421, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7307526327" }, { "job": 78640686378, "time": 369, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7307522084" }, { "job": 78640686375, "time": 440, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7307528124" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676886703", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/smoothclust", "_commit": { "id": "76b863ed5ef27dd6503d036912716f43dfd8c75c", "author": "Lukas Weber ", "committer": "Lukas Weber ", "message": "Merge branch 'apr2026-updates' into devel\n", "time": 1777406146 }, "_maintainer": { "name": "Lukas M. Weber", "email": "lmweb012@gmail.com", "login": "lmweber", "orcid": "0000-0002-3282-1730", "description": "Assistant Professor, Department of Biostatistics, Boston University", "uuid": 8062417 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "SpatialExperiment", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "BiocNeighbors", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "STexampleData", "role": "Suggests" }, { "package": "scuttle", "role": "Suggests" }, { "package": "scran", "role": "Suggests" }, { "package": "scater", "role": "Suggests" }, { "package": "ggspavis", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-36", "n": 1 }, { "week": "2025-38", "n": 6 }, { "week": "2025-44", "n": 3 }, { "week": "2026-17", "n": 4 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.9.1", "bioc": "3.24" }, { "branch": "release", "version": "1.8.0", "bioc": "3.23" } ], "_topics": [ "spatial", "singlecell", "transcriptomics", "geneexpression", "clustering" ], "_stars": 1, "_contributors": [ { "user": "lmweber", "count": 149, "uuid": 8062417 }, { "user": "jwokaty", "count": 10, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 279, "source": "https://www.bioconductor.org/packages/stats/bioc/smoothclust" }, "_devurl": "https://github.com/lmweber/smoothclust", "_searchresults": 13, "_rbuild": "4.6.0", "_assets": [ "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", "extra/smoothclust.html", "manual.pdf" ], "_homeurl": "https://github.com/lmweber/smoothclust", "_realowner": "bioc", "_cranurl": false, "_exports": [ "smoothclust", "smoothness_metric" ], "_help": [ { "page": "smoothclust", "title": "smoothclust", "topics": [ "smoothclust" ] }, { "page": "smoothness_metric", "title": "Function for smoothness metric", "topics": [ "smoothness_metric" ] } ], "_readme": "https://github.com/bioc/smoothclust/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "assorthead", "beachmat", "Biobase", "BiocFileCache", "BiocGenerics", "BiocNeighbors", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "curl", "DBI", "dbplyr", "DelayedArray", "dplyr", "fastmap", "filelock", "generics", "GenomicRanges", "glue", "httr2", "IRanges", "lattice", "lifecycle", "magick", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "openssl", "pillar", "pkgconfig", "purrr", "R6", "rappdirs", "Rcpp", "rjson", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "Seqinfo", "SingleCellExperiment", "SparseArray", "SpatialExperiment", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "XVector" ], "_vignettes": [ { "source": "smoothclust.Rmd", "filename": "smoothclust.html", "title": "Smoothclust Tutorial", "author": "Lukas M. Weber", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Input data format", "Tutorial", "Session information" ], "created": "2023-12-30 05:39:07", "modified": "2025-09-15 17:30:04", "commits": 26 } ], "_score": 4.511883360978874, "_indexed": true, "_nocasepkg": "smoothclust", "_universes": [ "bioc", "lmweber" ], "_previous": "1.9.0", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.9.1", "date": "2026-05-30T10:27:37.000Z", "distro": "noble", "commit": "76b863ed5ef27dd6503d036912716f43dfd8c75c", "fileid": "4e6cd84cfb47618115106e5714aceb1c53da18b4bb6af58284dd9bf4279897aa", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676886703" }, { "r": "4.6.0", "os": "linux", "version": "1.9.1", "date": "2026-05-30T10:27:45.000Z", "distro": "noble", "commit": "76b863ed5ef27dd6503d036912716f43dfd8c75c", "fileid": "9bb6d706fca2728c74212dab5e3736dbd735d7c9c7aac9f3d61e0fd8a5fc0d07", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676886703" }, { "r": "4.5.3", "os": "mac", "version": "1.9.1", "date": "2026-05-30T14:43:38.000Z", "commit": "76b863ed5ef27dd6503d036912716f43dfd8c75c", "fileid": "976f32474e5610160bb5b32d6dfebc6f86a393305375b2dc04b8ebf4e1f482a3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676886703" }, { "r": "4.6.0", "os": "mac", "version": "1.9.1", "date": "2026-05-30T14:44:26.000Z", "commit": "76b863ed5ef27dd6503d036912716f43dfd8c75c", "fileid": "73885c4319871777921ab0795ea09d05d1432819640a6f6b9ab9a9a3ff5aace0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676886703" }, { "r": "4.6.0", "os": "wasm", "version": "1.9.1", "date": "2026-05-30T10:26:53.000Z", "commit": "76b863ed5ef27dd6503d036912716f43dfd8c75c", "fileid": "b0712c1c9c12ab6e40e12cfdb3ca124581f0470347bf53ea45b291091b857a2e", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676886703" }, { "r": "4.7.0", "os": "win", "version": "1.9.1", "date": "2026-05-30T10:27:32.000Z", "commit": "76b863ed5ef27dd6503d036912716f43dfd8c75c", "fileid": "96639b427d43d62ad42c5dbd8146f5302002b0929dbde8b17783d71a763f90fb", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676886703" }, { "r": "4.5.3", "os": "win", "version": "1.9.1", "date": "2026-05-30T10:27:00.000Z", "commit": "76b863ed5ef27dd6503d036912716f43dfd8c75c", "fileid": "0dc538b435501a0513932311426cabda8cf94786a0beda7ca0fdd06ea1b3b1e5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676886703" }, { "r": "4.6.0", "os": "win", "version": "1.9.1", "date": "2026-05-30T10:28:00.000Z", "commit": "76b863ed5ef27dd6503d036912716f43dfd8c75c", "fileid": "fefad3e6b8e0d23b74fe60d0c5f02f7bcfd7cad8967f775e947b58d5d8d7c5a4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676886703" } ] }