{
  "_id": "6a3142f13efcd9bda4364b10",
  "Package": "BatchSVG",
  "Type": "Package",
  "Title": "Identify Batch-Biased Spatially Variable Genes",
  "Version": "1.4.0",
  "Authors@R": "c(person(\ngiven = \"Christine\",\nfamily = \"Hou\",\nrole = c(\"aut\"),\nemail = \"chris2018hou@gmail.com\",\ncomment = c(ORCID = \"0009-0001-5350-0629\")\n),\nc(person(\ngiven = \"Kinnary\",\nfamily = \"Shah\",\nrole = c(\"aut\", \"cre\"),\nemail = \"kinnaryshahh@gmail.com\")\n),\nperson(\ngiven = \"Jacqueline R.\",\nfamily = \"Thompson\",\nrole = \"aut\",\nemail = \"jthom338@jh.edu\"\n),\nperson(\ngiven = \"Stephanie C.\",\nfamily = \"Hicks\",\nrole = c(\"aut\",\"fnd\"),\nemail = \"shicks19@jhu.edu\",\ncomment = c(ORCID = \"0000-0002-7858-0231\"))\n)",
  "Description": "BatchSVG is a method to identify batch-biased spatially\nvariable genes (SVGs) in spatial transcriptomics data. The\nbatch variable can be defined as sample, donor sex, or other\nbatch effects of interest. The BatchSVG method is based on the\nbinomial deviance model (Townes et al, 2019).",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "biocViews": "Spatial, Transcriptomics, BatchEffect, QualityControl",
  "URL": "https://github.com/christinehou11/BatchSVG,\nhttps://christinehou11.github.io/BatchSVG",
  "BugReports": "https://github.com/christinehou11/BatchSVG/issues",
  "Config/testthat/edition": "3",
  "LazyData": "false",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 13:04:54 UTC",
  "RemoteUrl": "https://github.com/bioc/BatchSVG",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "402c3bd7e37792e0763d951076f063789d3ee88b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-16 11:57:36 UTC",
    "User": "root"
  },
  "Author": "Christine Hou [aut] (ORCID: <https://orcid.org/0009-0001-5350-0629>),\nKinnary Shah [aut, cre],\nJacqueline R. Thompson [aut],\nStephanie C. Hicks [aut, fnd] (ORCID:\n<https://orcid.org/0000-0002-7858-0231>)",
  "Maintainer": "Kinnary Shah <kinnaryshahh@gmail.com>",
  "MD5sum": "e33be0314a107b44c61a6358212b6f05",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "BatchSVG_1.4.0.tar.gz",
  "_fileid": "fd63417a25db286bcf6ad1e260a18b9ddc8afc605039601a3edbf8152ca3f353",
  "_filesize": 1507619,
  "_sha256": "fd63417a25db286bcf6ad1e260a18b9ddc8afc605039601a3edbf8152ca3f353",
  "_created": "2026-06-16T11:57:36.000Z",
  "_published": "2026-06-16T12:34:57.321Z",
  "_jobs": [
    {
      "job": 81651687717,
      "time": 286,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7666192775"
    },
    {
      "job": 81651687787,
      "time": 595,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7666306193"
    },
    {
      "job": 81651687736,
      "time": 587,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7666300974"
    },
    {
      "job": 81651687705,
      "time": 627,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7666314620"
    },
    {
      "job": 81651687754,
      "time": 625,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7666313654"
    },
    {
      "job": 81650000304,
      "time": 555,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7666080492"
    },
    {
      "job": 81651687721,
      "time": 231,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7666170378"
    },
    {
      "job": 81651687753,
      "time": 1888,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7666806392"
    },
    {
      "job": 81651687818,
      "time": 1860,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7666796005"
    },
    {
      "job": 81651687804,
      "time": 2090,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7666887152"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 4
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27615386198",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/BatchSVG",
  "_commit": {
    "id": "402c3bd7e37792e0763d951076f063789d3ee88b",
    "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": 1777381494
  },
  "_maintainer": {
    "name": "Kinnary Shah",
    "email": "kinnaryshahh@gmail.com",
    "login": "kinnaryshah",
    "linkedin": "in/kinnary-shah",
    "twitter": "@kinnaryhshah",
    "description": "working on spatial transcriptomics methods at JHU Biostat",
    "uuid": 89930321
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "scry",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "spatialLIBD",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-41",
      "n": 1
    },
    {
      "week": "2025-43",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2025-48",
      "n": 1
    },
    {
      "week": "2025-49",
      "n": 4
    },
    {
      "week": "2026-10",
      "n": 3
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.5.3",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.4.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "spatial",
    "transcriptomics",
    "batcheffect",
    "qualitycontrol",
    "batch-effect",
    "bioconductor-package",
    "spatial-transcriptomics"
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "kinnaryshah",
      "count": 11,
      "uuid": 89930321
    },
    {
      "user": "jwokaty",
      "count": 2,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 440,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/christinehou11/batchsvg",
  "_pkgdown": "https://christinehou11.github.io/BatchSVG",
  "_searchresults": 13,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/BatchSVG.html",
    "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",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/christinehou11/batchsvg",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "biasDetect",
    "featureSelect",
    "svg_nSD"
  ],
  "_datasets": [
    {
      "name": "list_batch_df",
      "title": "List of data frames of nSD(s) on the batch of subject",
      "object": "list_batch_df",
      "file": "list_batch_df.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "biasDetect",
      "title": "Biased Genes Identification",
      "topics": [
        "biasDetect"
      ]
    },
    {
      "page": "featureSelect",
      "title": "Feature selection",
      "topics": [
        "featureSelect"
      ]
    },
    {
      "page": "list_batch_df",
      "title": "List of data frames of nSD(s) on the batch of subject",
      "topics": [
        "list_batch_df"
      ]
    },
    {
      "page": "svg_nSD",
      "title": "SVGs Plots",
      "topics": [
        "svg_nSD"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/BatchSVG/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "assorthead",
    "beachmat",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "BiocSingular",
    "cli",
    "codetools",
    "cowplot",
    "cpp11",
    "DelayedArray",
    "dplyr",
    "farver",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "ggrepel",
    "glmpca",
    "glue",
    "gtable",
    "IRanges",
    "irlba",
    "isoband",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "pillar",
    "pkgconfig",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "rsvd",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "ScaledMatrix",
    "scales",
    "scry",
    "Seqinfo",
    "SingleCellExperiment",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "spe.Rmd",
      "filename": "spe.html",
      "title": "Find Batch-biased SVGs",
      "author": "Kinnary Shah, Christine Hou",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Biased Feature Identification",
        "Perform Feature Selection using featureSelect()",
        "Visualize SVG Selection Using svg_nSD()",
        "Identify Biased Genes Using biasDetect()",
        "Refine SVGs by Removing Batch-Affected Outliers",
        "R session information"
      ],
      "created": "2024-10-19 00:26:20",
      "modified": "2025-12-01 16:19:07",
      "commits": 32
    }
  ],
  "_score": 5.135132651376775,
  "_indexed": false,
  "_nocasepkg": "batchsvg",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/BatchSVG",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.4.0",
      "date": "2026-06-16T12:04:58.000Z",
      "distro": "noble",
      "commit": "402c3bd7e37792e0763d951076f063789d3ee88b",
      "fileid": "7ab4383aa0d1145f7dd3b152c8fcf11afd4aec7ad40fbcad119bd8a339057c57",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27615386198"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.4.0",
      "date": "2026-06-16T12:05:00.000Z",
      "distro": "noble",
      "commit": "402c3bd7e37792e0763d951076f063789d3ee88b",
      "fileid": "655ae918f1254fb7d1e1239e1d496ed2fed47b2577b4e344edc6c5197e6e8611",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27615386198"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.4.0",
      "date": "2026-06-16T12:02:11.000Z",
      "commit": "402c3bd7e37792e0763d951076f063789d3ee88b",
      "fileid": "8f2d3b195ebaef4fa2c2f053ba6c90bd61ef1edf7cb9416d906b2d42b22f2d52",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27615386198"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.4.0",
      "date": "2026-06-16T12:02:07.000Z",
      "commit": "402c3bd7e37792e0763d951076f063789d3ee88b",
      "fileid": "b3e4102c9532f59f92c5e801ece0c4bd1fdb0a64b83e3c0ee3446512d23476f4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27615386198"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.4.0",
      "date": "2026-06-16T12:03:34.000Z",
      "commit": "402c3bd7e37792e0763d951076f063789d3ee88b",
      "fileid": "d525c9bca48db760b1105ecbdc763e9b3e359073b1a8ab1ab04209e5e8d40d22",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27615386198"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.4.0",
      "date": "2026-06-16T12:25:40.000Z",
      "commit": "402c3bd7e37792e0763d951076f063789d3ee88b",
      "fileid": "59802fc06841034d0910982116a735fbee9f566b1001f84687db59cd4dc55ea9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27615386198"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.4.0",
      "date": "2026-06-16T12:25:09.000Z",
      "commit": "402c3bd7e37792e0763d951076f063789d3ee88b",
      "fileid": "66346951e9d512818db36597a05c912364dc116767c9220e7a9cb70015405a9b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27615386198"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.4.0",
      "date": "2026-06-16T12:29:09.000Z",
      "commit": "402c3bd7e37792e0763d951076f063789d3ee88b",
      "fileid": "dc6bff328d946534abe9f2fed7cb169457c844c4088bf5d80599bc97a55e0dcb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27615386198"
    }
  ]
}