{
  "_id": "6a1fdeffb401979e73438ebe",
  "Package": "batchelor",
  "Version": "1.28.0",
  "Date": "2026-04-09",
  "Title": "Single-Cell Batch Correction Methods",
  "Authors@R": "c(person(\"Aaron\", \"Lun\", role = c(\"aut\", \"cre\"), email = \"infinite.monkeys.with.keyboards@gmail.com\"),\nperson(\"Laleh\", \"Haghverdi\", role=\"ctb\"))",
  "biocViews": "Sequencing, RNASeq, Software, GeneExpression,\nTranscriptomics, SingleCell, BatchEffect, Normalization",
  "Description": "Implements a variety of methods for batch correction of\nsingle-cell (RNA sequencing) data. This includes methods based\non detecting mutually nearest neighbors, as well as several\nefficient variants of linear regression of the log-expression\nvalues. Functions are also provided to perform global rescaling\nto remove differences in depth between batches, and to perform\na principal components analysis that is robust to differences\nin the numbers of cells across batches.",
  "License": "GPL-3",
  "NeedsCompilation": "yes",
  "VignetteBuilder": "knitr",
  "SystemRequirements": "C++11",
  "RoxygenNote": "7.3.2",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:49:53 UTC",
  "RemoteUrl": "https://github.com/bioc/batchelor",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "5823437ffc4b954b83a9e0f26867da1d20fea268",
  "Packaged": {
    "Date": "2026-06-03 07:28:30 UTC",
    "User": "root"
  },
  "Author": "Aaron Lun [aut, cre],\nLaleh Haghverdi [ctb]",
  "Maintainer": "Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>",
  "MD5sum": "446a8aa1a265c0ef681698bc18b30217",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "batchelor_1.28.0.tar.gz",
  "_fileid": "462b3ad1df7d6188017b621ca64efab7709f8744e2e0fb09fad2bdf83d5b6e43",
  "_filesize": 1610036,
  "_sha256": "462b3ad1df7d6188017b621ca64efab7709f8744e2e0fb09fad2bdf83d5b6e43",
  "_created": "2026-06-03T07:28:30.000Z",
  "_published": "2026-06-03T07:59:59.106Z",
  "_jobs": [
    {
      "job": 79243542386,
      "time": 271,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7378361324"
    },
    {
      "job": 79243542403,
      "time": 436,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7378413708"
    },
    {
      "job": 79243542432,
      "time": 548,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7378449257"
    },
    {
      "job": 79243542398,
      "time": 479,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7378428239"
    },
    {
      "job": 79243542421,
      "time": 523,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7378441734"
    },
    {
      "job": 79243542413,
      "time": 413,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7378412316"
    },
    {
      "job": 79243542410,
      "time": 603,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7378467693"
    },
    {
      "job": 79243542443,
      "time": 422,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7378416809"
    },
    {
      "job": 79243542426,
      "time": 616,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7378471397"
    },
    {
      "job": 79242465491,
      "time": 444,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7378276628"
    },
    {
      "job": 79243542367,
      "time": 223,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7378346877"
    },
    {
      "job": 79243542364,
      "time": 1784,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7378860335"
    },
    {
      "job": 79243542470,
      "time": 1665,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7378819510"
    },
    {
      "job": 79243542411,
      "time": 1810,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7378870033"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 10
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26869917205",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/batchelor",
  "_commit": {
    "id": "5823437ffc4b954b83a9e0f26867da1d20fea268",
    "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": 1777380593
  },
  "_maintainer": {
    "name": "Aaron Lun",
    "email": "infinite.monkeys.with.keyboards@gmail.com",
    "login": "ltla",
    "twitter": "@realAaronLun",
    "description": "(ノಠ益ಠ)ノ彡┻━┻\n",
    "uuid": 8166669
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "SingleCellExperiment",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "BiocNeighbors",
      "role": "Imports"
    },
    {
      "package": "BiocSingular",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "SparseArray",
      "role": "Imports"
    },
    {
      "package": "DelayedArray",
      "version": ">= 0.31.5",
      "role": "Imports"
    },
    {
      "package": "DelayedMatrixStats",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "scuttle",
      "role": "Imports"
    },
    {
      "package": "ResidualMatrix",
      "role": "Imports"
    },
    {
      "package": "ScaledMatrix",
      "role": "Imports"
    },
    {
      "package": "beachmat",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "scran",
      "role": "Suggests"
    },
    {
      "package": "scater",
      "role": "Suggests"
    },
    {
      "package": "bluster",
      "role": "Suggests"
    },
    {
      "package": "scRNAseq",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 10,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-15",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.29.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.28.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "sequencing",
    "rnaseq",
    "software",
    "geneexpression",
    "transcriptomics",
    "singlecell",
    "batcheffect",
    "normalization",
    "cpp"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 7504,
    "source": "https://www.bioconductor.org/packages/stats/bioc/batchelor"
  },
  "_mentions": 9,
  "_searchresults": 1384,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/batchelor.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "applyMultiSCE",
    "batchCorrect",
    "checkBatchConsistency",
    "checkIfSCE",
    "checkRestrictions",
    "ClassicMnnParam",
    "clusterAbundanceTest",
    "clusterAbundanceVar",
    "clusterMNN",
    "convertPCsToSCE",
    "correctExperiments",
    "cosineNorm",
    "divideIntoBatches",
    "fastMNN",
    "FastMnnParam",
    "findMutualNN",
    "intersectRows",
    "mnnCorrect",
    "mnnDeltaVariance",
    "multiBatchNorm",
    "multiBatchPCA",
    "noCorrect",
    "NoCorrectParam",
    "quickCorrect",
    "reducedMNN",
    "regressBatches",
    "RegressParam",
    "rescaleBatches",
    "RescaleParam"
  ],
  "_help": [
    {
      "page": "applyMultiSCE",
      "title": "Apply function over multiple SingleCellExperiments",
      "topics": [
        "applyMultiSCE"
      ]
    },
    {
      "page": "batchCorrect",
      "title": "Batch correction methods",
      "topics": [
        "batchCorrect",
        "batchCorrect,ClassicMnnParam-method",
        "batchCorrect,FastMnnParam-method",
        "batchCorrect,NoCorrectParam-method",
        "batchCorrect,RegressParam-method",
        "batchCorrect,RescaleParam-method"
      ]
    },
    {
      "page": "batchelor-restrict",
      "title": "Using restriction",
      "topics": [
        "batchelor-restrict"
      ]
    },
    {
      "page": "BatchelorParam",
      "title": "BatchelorParam methods",
      "topics": [
        "BatchelorParam-class",
        "ClassicMnnParam",
        "ClassicMnnParam-class",
        "FastMnnParam",
        "FastMnnParam-class",
        "NoCorrectParam",
        "NoCorrectParam-class",
        "RegressParam",
        "RegressParam-class",
        "RescaleParam",
        "RescaleParam-class"
      ]
    },
    {
      "page": "checkInputs",
      "title": "Check batch inputs",
      "topics": [
        "checkBatchConsistency",
        "checkIfSCE",
        "checkRestrictions"
      ]
    },
    {
      "page": "clusterMNN",
      "title": "Cluster-based MNN",
      "topics": [
        "clusterMNN"
      ]
    },
    {
      "page": "convertPCsToSCE",
      "title": "Convert corrected PCs to a SingleCellExperiment",
      "topics": [
        "convertPCsToSCE"
      ]
    },
    {
      "page": "correctExperiments",
      "title": "Correct SingleCellExperiment objects",
      "topics": [
        "correctExperiments"
      ]
    },
    {
      "page": "cosineNorm",
      "title": "Cosine normalization",
      "topics": [
        "cosineNorm"
      ]
    },
    {
      "page": "diagnostics-cluster",
      "title": "Cluster-based correction diagnostics",
      "topics": [
        "clusterAbundanceTest",
        "clusterAbundanceVar",
        "diagnostics-cluster"
      ]
    },
    {
      "page": "divideIntoBatches",
      "title": "Divide into batches",
      "topics": [
        "divideIntoBatches"
      ]
    },
    {
      "page": "fastMNN",
      "title": "Fast mutual nearest neighbors correction",
      "topics": [
        "fastMNN"
      ]
    },
    {
      "page": "intersectRows",
      "title": "Take the intersection of rows across batches",
      "topics": [
        "intersectRows"
      ]
    },
    {
      "page": "mnnCorrect",
      "title": "Mutual nearest neighbors correction",
      "topics": [
        "mnnCorrect"
      ]
    },
    {
      "page": "mnnDeltaVariance",
      "title": "Computes the variance of the paired MNN deltas",
      "topics": [
        "mnnDeltaVariance"
      ]
    },
    {
      "page": "multiBatchNorm",
      "title": "Per-batch scaling normalization",
      "topics": [
        "multiBatchNorm"
      ]
    },
    {
      "page": "multiBatchPCA",
      "title": "Multi-batch PCA",
      "topics": [
        "multiBatchPCA"
      ]
    },
    {
      "page": "noCorrect",
      "title": "No correction",
      "topics": [
        "noCorrect"
      ]
    },
    {
      "page": "quickCorrect",
      "title": "Quickly perform batch correction",
      "topics": [
        "quickCorrect"
      ]
    },
    {
      "page": "reducedMNN",
      "title": "MNN correction in reduced dimensions",
      "topics": [
        "reducedMNN"
      ]
    },
    {
      "page": "regressBatches",
      "title": "Regress out batch effects",
      "topics": [
        "regressBatches"
      ]
    },
    {
      "page": "rescaleBatches",
      "title": "Scale counts across batches",
      "topics": [
        "rescaleBatches"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "assorthead",
    "beachmat",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocNeighbors",
    "BiocParallel",
    "BiocSingular",
    "cli",
    "codetools",
    "cpp11",
    "DelayedArray",
    "DelayedMatrixStats",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "glue",
    "igraph",
    "IRanges",
    "irlba",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "pkgconfig",
    "Rcpp",
    "ResidualMatrix",
    "rlang",
    "rsvd",
    "S4Arrays",
    "S4Vectors",
    "ScaledMatrix",
    "scuttle",
    "Seqinfo",
    "SingleCellExperiment",
    "snow",
    "SparseArray",
    "sparseMatrixStats",
    "SummarizedExperiment",
    "vctrs",
    "XVector"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "correction.Rmd",
      "filename": "correction.html",
      "title": "Correcting batch effects in single-cell RNA-seq data",
      "author": "Aaron Lun",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Setting up demonstration data",
        "Function organization",
        "Mutual nearest neighbors",
        "Overview",
        "The new, fast method",
        "The old, classic method",
        "The cluster-based method",
        "Batch rescaling",
        "Using data subsets",
        "Selecting genes",
        "Restricted correction",
        "Other utilities",
        "Multi-batch normalization",
        "Multi-batch PCA",
        "Session information",
        "References"
      ],
      "created": "2019-02-11 13:22:59",
      "modified": "2021-04-07 06:04:50",
      "commits": 10
    },
    {
      "source": "extension.Rmd",
      "filename": "extension.html",
      "title": "Extending dispatch to more batch correction methods",
      "author": "Aaron Lun",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Setting up",
        "Deriving a BatchelorParam subclass",
        "Defining a batchCorrect method",
        "Input",
        "Output",
        "Demonstration",
        "Session information"
      ],
      "created": "2019-02-11 16:18:42",
      "modified": "2019-11-02 05:54:24",
      "commits": 6
    }
  ],
  "_score": 9.22594393003438,
  "_indexed": false,
  "_nocasepkg": "batchelor",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/batchelor",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.28.0",
      "date": "2026-06-03T07:32:40.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "5823437ffc4b954b83a9e0f26867da1d20fea268",
      "fileid": "b2f1aea7e3f080f85bd8c372ad360b374c9ee924cc1d077de4f00a1cc77cc1be",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26869917205"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.28.0",
      "date": "2026-06-03T07:33:43.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "5823437ffc4b954b83a9e0f26867da1d20fea268",
      "fileid": "0959387cc8e9ec67449ad882b88f5fe02d8e3eea9a772b533cada3fe185e969d",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26869917205"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.28.0",
      "date": "2026-06-03T07:33:16.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "5823437ffc4b954b83a9e0f26867da1d20fea268",
      "fileid": "059cd1f44274ebb393c4253a5417f817d2d7179a690752d515c8721b7889e148",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26869917205"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.28.0",
      "date": "2026-06-03T07:33:34.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "5823437ffc4b954b83a9e0f26867da1d20fea268",
      "fileid": "4654f341d521df4b9ba59c890fe8d7af24d2f1ecd1210bb726dcf45d13b2e54f",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26869917205"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.28.0",
      "date": "2026-06-03T07:32:04.000Z",
      "arch": "aarch64",
      "commit": "5823437ffc4b954b83a9e0f26867da1d20fea268",
      "fileid": "b070309b076e6267ef0787c42c909df0a73572b78f24c0c553a5292ab67e8359",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26869917205"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.28.0",
      "date": "2026-06-03T07:33:37.000Z",
      "arch": "x86_64",
      "commit": "5823437ffc4b954b83a9e0f26867da1d20fea268",
      "fileid": "fc53fbdfd590ab79875bfc107f61f84105f5a9f8c4ca652a854ea2e2116fec13",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26869917205"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.28.0",
      "date": "2026-06-03T07:32:13.000Z",
      "arch": "aarch64",
      "commit": "5823437ffc4b954b83a9e0f26867da1d20fea268",
      "fileid": "8ca18c67d1e87527e7c7bcee50bb8cc2322151f0b04afe1419c7f202f20e3b90",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26869917205"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.28.0",
      "date": "2026-06-03T07:33:57.000Z",
      "arch": "x86_64",
      "commit": "5823437ffc4b954b83a9e0f26867da1d20fea268",
      "fileid": "d610ec138f0758ef6ea047a7a6de56d19f16b1b211f8bb4e3e0a7c171f534858",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26869917205"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.28.0",
      "date": "2026-06-03T07:32:52.000Z",
      "arch": "emscripten",
      "commit": "5823437ffc4b954b83a9e0f26867da1d20fea268",
      "fileid": "50abf05939f148828ff8aa7e065823e4de4393993fb76d279c218429ce113456",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26869917205"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.28.0",
      "date": "2026-06-03T07:53:59.000Z",
      "arch": "x86_64",
      "commit": "5823437ffc4b954b83a9e0f26867da1d20fea268",
      "fileid": "af5c2b99859f1f23696890aa77a8a13241c8986bfba502f0cb3bd5df08e94fb6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26869917205"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.28.0",
      "date": "2026-06-03T07:52:09.000Z",
      "arch": "x86_64",
      "commit": "5823437ffc4b954b83a9e0f26867da1d20fea268",
      "fileid": "68418e2d0cabe16e029e12549cf32b3ecec25d00fb21251a6920a6b2c8f2be2a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26869917205"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.28.0",
      "date": "2026-06-03T07:53:28.000Z",
      "arch": "x86_64",
      "commit": "5823437ffc4b954b83a9e0f26867da1d20fea268",
      "fileid": "c135073c90f133e9f102b5daf5c61041858ad276459a1390fb5ff0f208a1530f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26869917205"
    }
  ]
}