{
  "_id": "6a195f96acfb0bcc41de5591",
  "Package": "DenoIST",
  "Title": "DenoIST: Denoising Image-based Spatial Transcriptomics data",
  "Version": "1.0.0",
  "Authors@R": "c( \nperson(\"Aaron\", \"Kwok\", , \"akwok@svi.edu.au\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-7831-4198\")),\nperson(\"Heejung\",\"Shim\", role=c(\"aut\")),\nperson(\"Davis\",\"McCarthy\", role=c(\"aut\")))",
  "biocViews": "Software, Preprocessing, Spatial, GeneExpression,\nSingleCell, Transcriptomics",
  "Description": "DenoIST identifies and removes contamination in\nImage-based Spatial Transcriptomics data, using a transposed\npoisson mixture model with local neighbourhood offsets to infer\ngenes that are likely to be due to neighbourhood contamination\nrather than endogenous expression.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "URL": "https://github.com/aaronkwc/DenoIST",
  "BugReports": "https://github.com/aaronkwc/DenoIST/issues",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libmagick++-dev gsfonts libicu-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 13:06:20 UTC",
  "RemoteUrl": "https://github.com/bioc/DenoIST",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "391d87bc67c58cb52539a6cbf60568d841889831",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 08:04:27 UTC",
    "User": "root"
  },
  "Author": "Aaron Kwok [aut, cre] (ORCID: <https://orcid.org/0000-0001-7831-4198>),\nHeejung Shim [aut],\nDavis McCarthy [aut]",
  "Maintainer": "Aaron Kwok <akwok@svi.edu.au>",
  "MD5sum": "82a65a08151c26f2010351fb288f57cb",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "DenoIST_1.0.0.tar.gz",
  "_fileid": "dff454638c595747e2aec5a2d1388e8f05124676e6f0501562c00d577074ee97",
  "_filesize": 5551950,
  "_sha256": "dff454638c595747e2aec5a2d1388e8f05124676e6f0501562c00d577074ee97",
  "_created": "2026-05-29T08:04:27.000Z",
  "_published": "2026-05-29T09:42:46.939Z",
  "_jobs": [
    {
      "job": 78462248670,
      "time": 183,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286071403"
    },
    {
      "job": 78462248653,
      "time": 572,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7286178300"
    },
    {
      "job": 78462248690,
      "time": 615,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286190277"
    },
    {
      "job": 78462248644,
      "time": 260,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7287743978"
    },
    {
      "job": 78462248663,
      "time": 319,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7287765247"
    },
    {
      "job": 78461244267,
      "time": 431,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286020491"
    },
    {
      "job": 78462248667,
      "time": 139,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286059447"
    },
    {
      "job": 78462248685,
      "time": 1035,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7286311858"
    },
    {
      "job": 78462248672,
      "time": 792,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7286241335"
    },
    {
      "job": 78462248654,
      "time": 759,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286231497"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625526979",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/DenoIST",
  "_commit": {
    "id": "391d87bc67c58cb52539a6cbf60568d841889831",
    "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": 1777381580
  },
  "_maintainer": {
    "name": "Aaron Kwok",
    "email": "akwok@svi.edu.au",
    "orcid": "0000-0001-7831-4198"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "flexmix",
      "role": "Imports"
    },
    {
      "package": "hexbin",
      "role": "Imports"
    },
    {
      "package": "pbapply",
      "role": "Imports"
    },
    {
      "package": "sparseMatrixStats",
      "role": "Imports"
    },
    {
      "package": "SpatialExperiment",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "dbscan",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "patchwork",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-22",
      "n": 1
    },
    {
      "week": "2025-26",
      "n": 2
    },
    {
      "week": "2025-49",
      "n": 2
    },
    {
      "week": "2025-51",
      "n": 1
    },
    {
      "week": "2026-02",
      "n": 1
    },
    {
      "week": "2026-04",
      "n": 1
    },
    {
      "week": "2026-06",
      "n": 1
    },
    {
      "week": "2026-09",
      "n": 1
    },
    {
      "week": "2026-12",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.1.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.0.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "preprocessing",
    "spatial",
    "geneexpression",
    "singlecell",
    "transcriptomics"
  ],
  "_stars": 9,
  "_contributors": [
    {
      "user": "jwokaty",
      "count": 2,
      "uuid": 1744257
    },
    {
      "user": "dunstone-a",
      "count": 2,
      "uuid": 53158915
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 188,
    "source": "https://www.bioconductor.org/packages/stats/bioc/DenoIST"
  },
  "_devurl": "https://github.com/aaronkwc/denoist",
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/DenoIST.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/aaronkwc/denoist",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "denoist",
    "local_offset_distance_with_background",
    "local_offset_distance_with_background_fast",
    "solve_poisson_mixture"
  ],
  "_help": [
    {
      "page": "denoist",
      "title": "DenoIST",
      "topics": [
        "denoist"
      ]
    },
    {
      "page": "local_offset_distance_with_background",
      "title": "Neighbourhood offset",
      "topics": [
        "local_offset_distance_with_background"
      ]
    },
    {
      "page": "local_offset_distance_with_background_fast",
      "title": "Neighbourhood offset fast",
      "topics": [
        "local_offset_distance_with_background_fast"
      ]
    },
    {
      "page": "solve_poisson_mixture",
      "title": "Poisson mixture model solver",
      "topics": [
        "solve_poisson_mixture"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/DenoIST/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "cpp11",
    "curl",
    "DBI",
    "dbplyr",
    "dbscan",
    "DelayedArray",
    "dplyr",
    "fastmap",
    "filelock",
    "flexmix",
    "generics",
    "GenomicRanges",
    "glue",
    "hexbin",
    "httr2",
    "IRanges",
    "lattice",
    "lifecycle",
    "magick",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "modeltools",
    "nnet",
    "openssl",
    "pbapply",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "rappdirs",
    "Rcpp",
    "rjson",
    "rlang",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "SingleCellExperiment",
    "SparseArray",
    "sparseMatrixStats",
    "SpatialExperiment",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "denoist_spe.Rmd",
      "filename": "denoist_spe.html",
      "title": "Denoising Imaged-based Spatial Transcriptomics data with DenoIST",
      "author": "Aaron Kwok",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Load data",
        "Denoising the data",
        "Check results",
        "Session information"
      ],
      "created": "2025-05-20 09:02:17",
      "modified": "2026-02-06 07:16:45",
      "commits": 7
    }
  ],
  "_score": 5.653212513775344,
  "_indexed": false,
  "_nocasepkg": "denoist",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/DenoIST",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-05-29T08:07:32.000Z",
      "distro": "noble",
      "commit": "391d87bc67c58cb52539a6cbf60568d841889831",
      "fileid": "b576e8f98f57d75cb105c93b41a3666b141884ab85d3e4dc4ff55ce96e94a5a7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625526979"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-05-29T08:08:41.000Z",
      "distro": "noble",
      "commit": "391d87bc67c58cb52539a6cbf60568d841889831",
      "fileid": "2810c4cc5334ff9a47bb77c011bb3c531e470496ffb1989a76d80e83bfa6c2d0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625526979"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-05-29T09:38:09.000Z",
      "commit": "391d87bc67c58cb52539a6cbf60568d841889831",
      "fileid": "be2cae102d5f5fd6ec6d6c4e74248c5bb01be6b4f908e211127dd47271994e62",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625526979"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-05-29T09:38:23.000Z",
      "commit": "391d87bc67c58cb52539a6cbf60568d841889831",
      "fileid": "ab64316dbe3b71966611b6846d9fa856c8bf4edee4cb3a95d893171016ab7057",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625526979"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.0",
      "date": "2026-05-29T08:07:20.000Z",
      "commit": "391d87bc67c58cb52539a6cbf60568d841889831",
      "fileid": "ebe2034c29c4b05a197739a4bb2288a7afd468007cabc516f88394d875227846",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625526979"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-05-29T08:06:28.000Z",
      "commit": "391d87bc67c58cb52539a6cbf60568d841889831",
      "fileid": "64b95742f7e5472f9c666b5e196108c8f1dc4e0654af0892bcd2bde96350d39b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625526979"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-05-29T08:06:38.000Z",
      "commit": "391d87bc67c58cb52539a6cbf60568d841889831",
      "fileid": "2c64099501fe9606792c075bef181f0d911754e5f8d9ffd54f5d84385dcc91a0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625526979"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-05-29T08:06:06.000Z",
      "commit": "391d87bc67c58cb52539a6cbf60568d841889831",
      "fileid": "9a4c35714e59f2f29fca036d54e75fe2202932ac7df4bb0a8aa74bdf466e5603",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625526979"
    }
  ]
}