{
  "_id": "6ac8dac1de46216d5edd874e",
  "Package": "tpSVG",
  "Title": "Thin plate models to detect spatially variable genes",
  "Version": "1.9.0",
  "Authors@R": "c(\nperson(\"Boyi\", \"Guo\",\nemail = \"boyi.guo.work@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-2950-2349\")),\nperson(\"Lukas M.\", \"Weber\",\nemail = \"lukas.weber.edu@gmail.com\",\nrole = c(\"ctb\"),\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\")))",
  "Description": "The goal of `tpSVG` is to detect and visualize spatial\nvariation in the gene expression for spatially resolved\ntranscriptomics data analysis. Specifically, `tpSVG` introduces\na family of count-based models, with generalizable parametric\nassumptions such as Poisson distribution or negative binomial\ndistribution. In addition, comparing to currently available\ncount-based model for spatially resolved data analysis, the\n`tpSVG` models improves computational time, and hence greatly\nimproves the applicability of count-based models in SRT data\nanalysis.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/boyiguo1/tpSVG",
  "BugReports": "https://github.com/boyiguo1/tpSVG/issues",
  "biocViews": "Spatial, Transcriptomics, GeneExpression, Software,\nStatisticalMethod, DimensionReduction, Regression,\nPreprocessing",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.2.3",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "libmagick++-dev gsfonts libicu-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:02:29 UTC",
  "RemoteUrl": "https://github.com/bioc/tpSVG",
  "RemoteRef": "HEAD",
  "RemoteSha": "7145726ee2fcd03d756fa9d82943458bfbba22bf",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-09 12:06:53 UTC",
    "User": "root"
  },
  "Author": "Boyi Guo [aut, cre] (ORCID: <https://orcid.org/0000-0003-2950-2349>),\nLukas M. Weber [ctb] (ORCID: <https://orcid.org/0000-0002-3282-1730>),\nStephanie C. Hicks [aut] (ORCID:\n<https://orcid.org/0000-0002-7858-0231>)",
  "Maintainer": "Boyi Guo <boyi.guo.work@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "tpSVG_1.9.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/a4b0623f2d6c3643350dd7ba3cb04706ccf261b5310ecd180487d3dadc5d8003",
  "_filesize": 1166546,
  "_sha256": "a4b0623f2d6c3643350dd7ba3cb04706ccf261b5310ecd180487d3dadc5d8003",
  "_expires": "2027-01-17T12:14:55.000Z",
  "_created": "2026-10-09T12:06:53.000Z",
  "_published": "2026-10-09T12:14:57.377Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/37927385553",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 5
  },
  "_upstream": "https://github.com/bioc/tpSVG",
  "_commit": {
    "id": "7145726ee2fcd03d756fa9d82943458bfbba22bf",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381349
  },
  "_maintainer": {
    "name": "Boyi Guo",
    "email": "boyi.guo.work@gmail.com",
    "login": "boyiguo1",
    "orcid": "0000-0003-2950-2349",
    "twitter": "@BoyiGuo",
    "description": "Biostatistician, Omics data scientist",
    "uuid": 16565218
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 113811503592,
      "time": 198,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11614369723"
    },
    {
      "job": 113811504109,
      "time": 423,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11614902123"
    },
    {
      "job": 113811503768,
      "time": 419,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11615066915"
    },
    {
      "job": 113811503780,
      "time": 254,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11615610046"
    },
    {
      "job": 113811503659,
      "time": 192,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11614966514"
    },
    {
      "job": 113809583258,
      "time": 330,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11614851974"
    },
    {
      "job": 113811503709,
      "time": 169,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11614767665"
    },
    {
      "job": 113811503706,
      "time": 378,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11615016952"
    },
    {
      "job": 113811503754,
      "time": 409,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11615755329"
    },
    {
      "job": 113811503808,
      "time": 375,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11615096758"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "mgcv",
      "role": "Depends"
    },
    {
      "package": "R",
      "version": ">= 4.4",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "MatrixGenerics",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "SpatialExperiment",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "nnSVG",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "scran",
      "role": "Suggests"
    },
    {
      "package": "scuttle",
      "role": "Suggests"
    },
    {
      "package": "STexampleData",
      "role": "Suggests"
    },
    {
      "package": "escheR",
      "role": "Suggests"
    },
    {
      "package": "ggpubr",
      "role": "Suggests"
    },
    {
      "package": "colorspace",
      "role": "Suggests"
    },
    {
      "package": "BumpyMatrix",
      "role": "Suggests"
    },
    {
      "package": "sessioninfo",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.9.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.8.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "spatial",
    "transcriptomics",
    "geneexpression",
    "software",
    "statisticalmethod",
    "dimensionreduction",
    "regression",
    "preprocessing",
    "spatially-resolve",
    "spatially-variable-genes"
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "boyiguo1",
      "count": 109,
      "uuid": 16565218
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 475,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 270,
    "source": "https://www.bioconductor.org/packages/stats/bioc/tpSVG"
  },
  "_devurl": "https://github.com/boyiguo1/tpsvg",
  "_searchresults": 2,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/tpSVG.html",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/boyiguo1/tpsvg",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "tpSVG"
  ],
  "_help": [
    {
      "page": "tpSVG",
      "title": "Thin Plate Spline Model to Detect Spatially Variable Genes",
      "topics": [
        "tpSVG"
      ]
    }
  ],
  "_pkglogo": "https://github.com/bioc/tpSVG/raw/HEAD/logo.png",
  "_readme": "https://github.com/bioc/tpSVG/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "BH",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "BiocParallel",
    "bit",
    "bit64",
    "blob",
    "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",
    "mgcv",
    "nlme",
    "openssl",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "Rcpp",
    "rjson",
    "rlang",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "SingleCellExperiment",
    "snow",
    "SparseArray",
    "SpatialExperiment",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "intro_to_tpSVG.Rmd",
      "filename": "intro_to_tpSVG.html",
      "title": "Introduction to tpSVG",
      "author": "Boyi Guo",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "GitHub",
        "Bioconductor (pending)",
        "Modeling spatially resolved gene expression using tpSVG",
        "Load Packages",
        "Data processing",
        "Modeling raw counts with Poisson model",
        "Gaussian model for log-transformed normalized data",
        "Covariate-adjusted Model",
        "image-based SRT in SpatialExperiment (e.g. SpatialFeatureExperiment)",
        "Session Info"
      ],
      "created": "2023-04-15 15:19:50",
      "modified": "2024-02-28 16:42:24",
      "commits": 5
    }
  ],
  "_score": 4.301029995663981,
  "_indexed": true,
  "_nocasepkg": "tpsvg",
  "_universes": [
    "bioc",
    "boyiguo1"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.9.0",
      "date": "2026-10-09T12:11:47.000Z",
      "distro": "resolute",
      "commit": "7145726ee2fcd03d756fa9d82943458bfbba22bf",
      "fileid": "https://r2.ropensci.org/81b274637c34447695580985c3cec32b1a41aa67ccd5ecc8bd0c4557750f5356",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37927385553"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.9.0",
      "date": "2026-10-09T12:11:48.000Z",
      "distro": "resolute",
      "commit": "7145726ee2fcd03d756fa9d82943458bfbba22bf",
      "fileid": "https://r2.ropensci.org/495bc6a247d72aa98d4131f39c5bd2c50f928e3bfcdb2bcfba387a33280ae1e4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37927385553"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.9.0",
      "date": "2026-10-09T12:09:21.000Z",
      "commit": "7145726ee2fcd03d756fa9d82943458bfbba22bf",
      "fileid": "https://r2.ropensci.org/eb2787f32202128bb8a01bd46fb6a1488c0d1036bf219174ec944b84ca30b048",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37927385553"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.9.0",
      "date": "2026-10-09T12:09:04.000Z",
      "commit": "7145726ee2fcd03d756fa9d82943458bfbba22bf",
      "fileid": "https://r2.ropensci.org/97ac6aae6e01dca969a6d441fb2285c16d5be863b62bea3066d34e7fd6b313cd",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37927385553"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.9.0",
      "date": "2026-10-09T12:10:16.000Z",
      "commit": "7145726ee2fcd03d756fa9d82943458bfbba22bf",
      "fileid": "https://r2.ropensci.org/37e8acaba9fef8bcbfb05471db9ec8968f0bd096404881ce3e191630cb5917ed",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37927385553"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-10-09T12:10:51.000Z",
      "commit": "7145726ee2fcd03d756fa9d82943458bfbba22bf",
      "fileid": "https://r2.ropensci.org/b37608d6c7a6da7e48c3ea8bc1543d9f21500a3dfdd51e83722d75e2c760cd90",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37927385553"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-10-09T12:11:30.000Z",
      "commit": "7145726ee2fcd03d756fa9d82943458bfbba22bf",
      "fileid": "https://r2.ropensci.org/31b201b63c7d7ca1c0df66471e848e590e1d01535270d552669003d5a30eb0dd",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37927385553"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-10-09T12:11:01.000Z",
      "commit": "7145726ee2fcd03d756fa9d82943458bfbba22bf",
      "fileid": "https://r2.ropensci.org/0dd66cfce57e3ae110dcac33294980ba12d2f43d7b36f5ce2c21fc7c484b30be",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37927385553"
    }
  ]
}