{
  "_id": "6a2cf49d3efcd9bda42e4545",
  "Package": "clustSIGNAL",
  "Type": "Package",
  "Title": "ClustSIGNAL: a spatial clustering method",
  "Version": "1.4.0",
  "Authors@R": "c(\nperson(\"Pratibha\", \"Panwar\", email = \"pratibhapanwar.4@gmail.com\",\nrole = c(\"cre\", \"aut\", \"ctb\"), comment = c(ORCID = \"0000-0002-7437-7084\")),\nperson(\"Boyi\", \"Guo\", email = \"boyi.guo.work@gmail.com\", role = \"aut\"),\nperson(\"Haowen\", \"Zhao\", email = \"haowen.zhou19@gmail.com\", role = \"aut\"),\nperson(\"Stephanie\", \"Hicks\", email = \"shicks19@jhu.edu\", role = \"aut\"),\nperson(\"Shila\", \"Ghazanfar\", email = \"shazanfar@gmail.com\",\nrole = c(\"aut\", \"ctb\"), comment = c(ORCID = \"0000-0001-7861-6997\")))",
  "Description": "clustSIGNAL: clustering of Spatially Informed Gene\nexpression with Neighbourhood Adapted Learning. A tool for\nadaptively smoothing and clustering gene expression data.\nclustSIGNAL uses entropy to measure heterogeneity of cell\nneighbourhoods and performs a weighted, adaptive smoothing,\nwhere homogeneous neighbourhoods are smoothed more and\nheterogeneous neighbourhoods are smoothed less. This not only\novercomes data sparsity but also incorporates spatial context\ninto the gene expression data. The resulting smoothed gene\nexpression data is used for clustering and could be used for\nother downstream analyses.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "URL": "https://sydneybiox.github.io/clustSIGNAL/",
  "BugReports": "https://github.com/sydneybiox/clustSIGNAL/issues",
  "biocViews": "Clustering, Software, GeneExpression, Spatial,\nTranscriptomics, SingleCell",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libcairo2-dev libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev libglpk-dev libharfbuzz-dev libmagick++-dev\ngsfonts libicu-dev libjpeg-dev libpng-dev libtiff-dev\nlibwebp-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 13:04:52 UTC",
  "RemoteUrl": "https://github.com/bioc/clustSIGNAL",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "420ae66f7ddba00961016e6f13552ba449611db5",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-13 06:03:37 UTC",
    "User": "root"
  },
  "Author": "Pratibha Panwar [cre, aut, ctb] (ORCID:\n<https://orcid.org/0000-0002-7437-7084>),\nBoyi Guo [aut],\nHaowen Zhao [aut],\nStephanie Hicks [aut],\nShila Ghazanfar [aut, ctb] (ORCID:\n<https://orcid.org/0000-0001-7861-6997>)",
  "Maintainer": "Pratibha Panwar <pratibhapanwar.4@gmail.com>",
  "MD5sum": "723f469c8ece58614b784845a9d60e3f",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "clustSIGNAL_1.4.0.tar.gz",
  "_fileid": "3eeada6f5061baf88dbf073a860b07175ead9439e7696a9d252c178c66e7cf34",
  "_filesize": 3529322,
  "_sha256": "3eeada6f5061baf88dbf073a860b07175ead9439e7696a9d252c178c66e7cf34",
  "_created": "2026-06-13T06:03:37.000Z",
  "_published": "2026-06-13T06:11:41.770Z",
  "_jobs": [
    {
      "job": 81167661596,
      "time": 207,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7608003256"
    },
    {
      "job": 81167661595,
      "time": 361,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7608022233"
    },
    {
      "job": 81167661586,
      "time": 419,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7608029500"
    },
    {
      "job": 81167661589,
      "time": 275,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7608012045"
    },
    {
      "job": 81167661606,
      "time": 199,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7608002088"
    },
    {
      "job": 81167331007,
      "time": 314,
      "config": "source",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7607976517"
    },
    {
      "job": 81167661599,
      "time": 171,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7607998576"
    },
    {
      "job": 81167661604,
      "time": 404,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7608027660"
    },
    {
      "job": 81167661594,
      "time": 344,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7608020431"
    },
    {
      "job": 81167661612,
      "time": 307,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7608016161"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329825116",
  "_status": "failure",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/clustSIGNAL",
  "_commit": {
    "id": "420ae66f7ddba00961016e6f13552ba449611db5",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777381492
  },
  "_maintainer": {
    "name": "Pratibha Panwar",
    "email": "pratibhapanwar.4@gmail.com",
    "login": "pratibhapanwar",
    "linkedin": "in/pratibha-panwar-49027225a",
    "orcid": "0000-0002-7437-7084",
    "description": "",
    "uuid": 7644123
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4.0",
      "role": "Depends"
    },
    {
      "package": "SpatialExperiment",
      "role": "Depends"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "BiocNeighbors",
      "role": "Imports"
    },
    {
      "package": "bluster",
      "version": ">= 1.16.0",
      "role": "Imports"
    },
    {
      "package": "scater",
      "role": "Imports"
    },
    {
      "package": "harmony",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "aricode",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "patchwork",
      "role": "Suggests"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    },
    {
      "package": "scattermore",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-42",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.5.1",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.4.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "clustering",
    "software",
    "geneexpression",
    "spatial",
    "transcriptomics",
    "singlecell"
  ],
  "_stars": 6,
  "_contributors": [
    {
      "user": "pratibhapanwar",
      "count": 155,
      "uuid": 7644123
    },
    {
      "user": "jwokaty",
      "count": 4,
      "uuid": 1744257
    },
    {
      "user": "shazanfar",
      "count": 3,
      "uuid": 12996210
    },
    {
      "user": "hpages",
      "count": 1,
      "uuid": 8810451
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 253,
    "source": "https://www.bioconductor.org/packages/stats/bioc/clustSIGNAL"
  },
  "_devurl": "https://github.com/sydneybiox/clustsignal",
  "_pkgdown": "https://sydneybiox.github.io/clustSIGNAL/",
  "_searchresults": 3,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/clustSIGNAL.html",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/sydneybiox/clustsignal",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "adaptiveSmoothing",
    "clustSIGNAL",
    "entropyMeasure",
    "neighbourDetect",
    "p1_clustering",
    "p2_clustering"
  ],
  "_datasets": [
    {
      "name": "me_data",
      "title": "Mouse Embryo Data",
      "object": "mEmbryo2",
      "file": "mEmbryo2.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "uniqueID",
        "pos",
        "celltype_mapped_refined",
        "sample_id",
        "X",
        "Y"
      ],
      "rows": 5000,
      "table": true,
      "tojson": true
    },
    {
      "name": "me_expr",
      "title": "Mouse Embryo Data",
      "object": "mEmbryo2",
      "file": "mEmbryo2.RData",
      "class": [
        "dgCMatrix"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mh_data",
      "title": "Mouse Hypothalamus Data",
      "object": "mHypothal",
      "file": "mHypothal.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Cell_ID",
        "Cell_class",
        "sample_id",
        "samples",
        "X",
        "Y"
      ],
      "rows": 6000,
      "table": true,
      "tojson": true
    },
    {
      "name": "mh_expr",
      "title": "Mouse Hypothalamus Data",
      "object": "mHypothal",
      "file": "mHypothal.RData",
      "class": [
        "dgCMatrix"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "nnCells",
      "title": "Example data with SpatialExperiment object",
      "object": "ClustSignal_example",
      "file": "ClustSignal_example.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": {},
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "regXclust",
      "title": "Example data with SpatialExperiment object",
      "object": "ClustSignal_example",
      "file": "ClustSignal_example.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": false
    },
    {
      "name": "spe",
      "title": "Example data with SpatialExperiment object",
      "object": "ClustSignal_example",
      "file": "ClustSignal_example.RData",
      "class": [
        "SpatialExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "adaptiveSmoothing",
      "title": "Adaptive smoothing",
      "topics": [
        "adaptiveSmoothing"
      ]
    },
    {
      "page": "clustSIGNAL",
      "title": "ClustSIGNAL",
      "topics": [
        "clustSIGNAL"
      ]
    },
    {
      "page": "ClustSignal_example",
      "title": "Example data with SpatialExperiment object",
      "topics": [
        "ClustSignal_example",
        "nnCells",
        "regXclust",
        "spe"
      ]
    },
    {
      "page": "entropyMeasure",
      "title": "Heterogeneity measure",
      "topics": [
        "entropyMeasure"
      ]
    },
    {
      "page": "mEmbryo2",
      "title": "Mouse Embryo Data",
      "topics": [
        "mEmbryo2",
        "me_data",
        "me_expr"
      ]
    },
    {
      "page": "mHypothal",
      "title": "Mouse Hypothalamus Data",
      "topics": [
        "mHypothal",
        "mh_data",
        "mh_expr"
      ]
    },
    {
      "page": "neighbourDetect",
      "title": "Cell neighbourhood detection",
      "topics": [
        "neighbourDetect"
      ]
    },
    {
      "page": "p1_clustering",
      "title": "Initial non-spatial clustering",
      "topics": [
        "p1_clustering"
      ]
    },
    {
      "page": "p2_clustering",
      "title": "Final non-spatial clustering",
      "topics": [
        "p2_clustering"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/clustSIGNAL/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "assorthead",
    "base64enc",
    "beachmat",
    "beeswarm",
    "BH",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "BiocNeighbors",
    "BiocParallel",
    "BiocSingular",
    "bit",
    "bit64",
    "blob",
    "bluster",
    "cachem",
    "Cairo",
    "cli",
    "cluster",
    "codetools",
    "cowplot",
    "cpp11",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dplyr",
    "dqrng",
    "farver",
    "fastmap",
    "filelock",
    "FNN",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggbeeswarm",
    "ggplot2",
    "ggrastr",
    "ggrepel",
    "glue",
    "gridExtra",
    "gtable",
    "harmony",
    "httr2",
    "igraph",
    "IRanges",
    "irlba",
    "isoband",
    "jsonlite",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magick",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "openssl",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "purrr",
    "R6",
    "ragg",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppAnnoy",
    "RcppArmadillo",
    "RcppEigen",
    "RcppML",
    "RcppProgress",
    "reshape2",
    "RhpcBLASctl",
    "rjson",
    "rlang",
    "RSpectra",
    "RSQLite",
    "rsvd",
    "Rtsne",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "ScaledMatrix",
    "scales",
    "scater",
    "scuttle",
    "Seqinfo",
    "SingleCellExperiment",
    "sitmo",
    "snow",
    "SparseArray",
    "SpatialExperiment",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "systemfonts",
    "textshaping",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "uwot",
    "vctrs",
    "vipor",
    "viridis",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_score": 4.431363764158988,
  "_indexed": false,
  "_nocasepkg": "clustsignal",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/clustSIGNAL",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.4.0",
      "date": "2026-06-13T06:07:21.000Z",
      "distro": "noble",
      "commit": "420ae66f7ddba00961016e6f13552ba449611db5",
      "fileid": "ecae1f4234a338f91013384722b9d4816f10710c9392800efa10186b0e1b2b74",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329825116"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.4.0",
      "date": "2026-06-13T06:08:12.000Z",
      "distro": "noble",
      "commit": "420ae66f7ddba00961016e6f13552ba449611db5",
      "fileid": "a70ed28f077a9a6282338b301279f0b2004d22f70d4f387f238bc6007fea9f65",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329825116"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.4.0",
      "date": "2026-06-13T06:06:07.000Z",
      "commit": "420ae66f7ddba00961016e6f13552ba449611db5",
      "fileid": "ffbf71dcdaca7b03a7d09fb1d3770cb68723b8cfb297138cbcfe972a2d0d1452",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329825116"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.4.0",
      "date": "2026-06-13T06:05:49.000Z",
      "commit": "420ae66f7ddba00961016e6f13552ba449611db5",
      "fileid": "84d0ab643d269a92c0700b46cd797ecf7194edd19d7a4c9cd5110129484ac338",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329825116"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.4.0",
      "date": "2026-06-13T06:07:04.000Z",
      "commit": "420ae66f7ddba00961016e6f13552ba449611db5",
      "fileid": "b9ddda6fe73694f3d25838dfea02fe1975b534d4debf2879759ba2c2263a9513",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329825116"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.4.0",
      "date": "2026-06-13T06:07:55.000Z",
      "commit": "420ae66f7ddba00961016e6f13552ba449611db5",
      "fileid": "bbdfe191c1ffca89130da093c1ee8b1c1b2ec012d341e4f3c9dd4479fd7fb410",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329825116"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.4.0",
      "date": "2026-06-13T06:06:59.000Z",
      "commit": "420ae66f7ddba00961016e6f13552ba449611db5",
      "fileid": "fbb06f6ef3bf8e3577884df0c22a5c37b78f3e68fdaf2e7350b1f2a06f1eb03f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329825116"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.4.0",
      "date": "2026-06-13T06:06:23.000Z",
      "commit": "420ae66f7ddba00961016e6f13552ba449611db5",
      "fileid": "201f5627d71054a1b2a62dd3a3715989b98a93592106f22268d491be4b548c59",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329825116"
    }
  ]
}