{
  "_id": "6a19727dacfb0bcc41deebc2",
  "Package": "nnSVG",
  "Version": "1.16.0",
  "Title": "Scalable identification of spatially variable genes in\nspatially-resolved transcriptomics data",
  "Description": "Method for scalable identification of spatially variable\ngenes (SVGs) in spatially-resolved transcriptomics data. The\nmethod is based on nearest-neighbor Gaussian processes and uses\nthe BRISC algorithm for model fitting and parameter estimation.\nAllows identification and ranking of SVGs with flexible length\nscales across a tissue slide or within spatial domains defined\nby covariates. Scales linearly with the number of spatial\nlocations and can be applied to datasets containing thousands\nor more spatial locations.",
  "Authors@R": "c(\nperson(\"Lukas M.\", \"Weber\",\nemail = \"lmweb012@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-3282-1730\")),\nperson(\"Stephanie C.\", \"Hicks\",\nemail = \"shicks19@jhu.edu\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-7858-0231\")))",
  "URL": "https://github.com/lmweber/nnSVG",
  "BugReports": "https://github.com/lmweber/nnSVG/issues",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "biocViews": "Spatial, SingleCell, Transcriptomics, GeneExpression,\nPreprocessing",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.2.3",
  "Config/pak/sysreqs": "libmagick++-dev gsfonts libicu-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:58:01 UTC",
  "RemoteUrl": "https://github.com/bioc/nnSVG",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "1a64b2636efd71953073acf4f9f33eb274a39780",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 09:03:05 UTC",
    "User": "root"
  },
  "Author": "Lukas M. Weber [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-3282-1730>),\nStephanie C. Hicks [aut] (ORCID:\n<https://orcid.org/0000-0002-7858-0231>)",
  "Maintainer": "Lukas M. Weber <lmweb012@gmail.com>",
  "MD5sum": "756ee426d659b8c0a26bcaf8646a3b72",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "nnSVG_1.16.0.tar.gz",
  "_fileid": "cac935835b5798f5f1eea08b44e4ef12bf89c8a496e1ae7ed09230828caf0d0a",
  "_filesize": 1446471,
  "_sha256": "cac935835b5798f5f1eea08b44e4ef12bf89c8a496e1ae7ed09230828caf0d0a",
  "_created": "2026-05-29T09:03:05.000Z",
  "_published": "2026-05-29T11:03:25.378Z",
  "_jobs": [
    {
      "job": 78470785476,
      "time": 239,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7287127521"
    },
    {
      "job": 78470785450,
      "time": 598,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7287233840"
    },
    {
      "job": 78470785509,
      "time": 502,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7287205793"
    },
    {
      "job": 78470785418,
      "time": 292,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7289153915"
    },
    {
      "job": 78470785413,
      "time": 284,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7289156450"
    },
    {
      "job": 78469418574,
      "time": 541,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7287054755"
    },
    {
      "job": 78470785423,
      "time": 205,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7287116972"
    },
    {
      "job": 78470785448,
      "time": 509,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7287207591"
    },
    {
      "job": 78470785435,
      "time": 478,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7287198454"
    },
    {
      "job": 78470785447,
      "time": 490,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7287202196"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627994059",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/nnSVG",
  "_commit": {
    "id": "1a64b2636efd71953073acf4f9f33eb274a39780",
    "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": 1777381081
  },
  "_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": ">= 4.2",
      "role": "Depends"
    },
    {
      "package": "SpatialExperiment",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "BRISC",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "STexampleData",
      "role": "Suggests"
    },
    {
      "package": "WeberDivechaLCdata",
      "role": "Suggests"
    },
    {
      "package": "scran",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.17.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.16.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "spatial",
    "singlecell",
    "transcriptomics",
    "geneexpression",
    "preprocessing"
  ],
  "_stars": 24,
  "_contributors": [
    {
      "user": "lmweber",
      "count": 279,
      "uuid": 8062417
    },
    {
      "user": "jwokaty",
      "count": 12,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 2,
      "uuid": 2746443
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 490,
    "source": "https://www.bioconductor.org/packages/stats/bioc/nnSVG"
  },
  "_devurl": "https://github.com/lmweber/nnsvg",
  "_searchresults": 346,
  "_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/nnSVG.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/lmweber/nnsvg",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "filter_genes",
    "nnSVG"
  ],
  "_help": [
    {
      "page": "filter_genes",
      "title": "Preprocessing function to filter genes",
      "topics": [
        "filter_genes"
      ]
    },
    {
      "page": "nnSVG",
      "title": "nnSVG",
      "topics": [
        "nnSVG"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/nnSVG/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "BH",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "BiocParallel",
    "bit",
    "bit64",
    "blob",
    "BRISC",
    "cachem",
    "cli",
    "codetools",
    "cpp11",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dplyr",
    "fastmap",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "glue",
    "httr2",
    "IRanges",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magick",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "openssl",
    "pbapply",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "RANN",
    "rappdirs",
    "Rcpp",
    "RcppArmadillo",
    "rdist",
    "rjson",
    "rlang",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "SingleCellExperiment",
    "snow",
    "SparseArray",
    "SpatialExperiment",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "nnSVG.Rmd",
      "filename": "nnSVG.html",
      "title": "nnSVG Tutorial",
      "author": "Lukas M. Weber, Stephanie C. Hicks",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Input data format",
        "Tutorial",
        "Standard analysis",
        "Run nnSVG",
        "Investigate results",
        "With covariates",
        "Multiple samples",
        "Troubleshooting",
        "Zeros (genes or spots)",
        "Small numbers of spots",
        "Session information"
      ],
      "created": "2021-09-27 17:58:38",
      "modified": "2025-02-07 22:30:47",
      "commits": 63
    }
  ],
  "_score": 7.6974385908880265,
  "_indexed": false,
  "_nocasepkg": "nnsvg",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/nnSVG",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.16.0",
      "date": "2026-05-29T09:08:48.000Z",
      "distro": "noble",
      "commit": "1a64b2636efd71953073acf4f9f33eb274a39780",
      "fileid": "58c4f4958f619f4740dfe4c549fab18ddf4e3cf79cb8dd22be97c193e5aa2fb4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627994059"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.16.0",
      "date": "2026-05-29T09:07:24.000Z",
      "distro": "noble",
      "commit": "1a64b2636efd71953073acf4f9f33eb274a39780",
      "fileid": "6a1828401a1c28c210370182851a878269de79ebb1237e0558378ae8bfacc28f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627994059"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.16.0",
      "date": "2026-05-29T10:59:57.000Z",
      "commit": "1a64b2636efd71953073acf4f9f33eb274a39780",
      "fileid": "f32684df6a9470af370e03757ab32a1e8ea6c8f989a02de9918ff1f51157f4e1",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627994059"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.16.0",
      "date": "2026-05-29T11:00:14.000Z",
      "commit": "1a64b2636efd71953073acf4f9f33eb274a39780",
      "fileid": "5ffa139cfaebe649822bb8909d2a9ef1491aa3fa41a004713716b4d4fcbfd1b9",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627994059"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.16.0",
      "date": "2026-05-29T09:07:00.000Z",
      "commit": "1a64b2636efd71953073acf4f9f33eb274a39780",
      "fileid": "b12ea89b7b25d4baf0a6a77e28df5bff65fe5f24c1684ac99b0d46dda638bb8f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627994059"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.16.0",
      "date": "2026-05-29T09:06:51.000Z",
      "commit": "1a64b2636efd71953073acf4f9f33eb274a39780",
      "fileid": "90c7a5b86d8f54fe736453727fdb19e66e01b20fc7ea6c6e0a3a8aec2eefd79d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627994059"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.16.0",
      "date": "2026-05-29T09:07:00.000Z",
      "commit": "1a64b2636efd71953073acf4f9f33eb274a39780",
      "fileid": "f6085763d3168cd7088f3ae6031989eedf3788b437267f180a96ef323951815c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627994059"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.16.0",
      "date": "2026-05-29T09:06:55.000Z",
      "commit": "1a64b2636efd71953073acf4f9f33eb274a39780",
      "fileid": "2317ce1529a504a0e9afa9d02019f2349c7a98e043ffe1dae22363549dbbc12c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627994059"
    }
  ]
}