{
  "_id": "6a10247eacfb0bcc41c8dc9f",
  "Package": "mumosa",
  "Type": "Package",
  "Authors@R": "person(\"Aaron\", \"Lun\", role = c(\"aut\", \"cre\"), email=\"infinite.monkeys.with.keyboards@gmail.com\")",
  "Version": "1.21.0",
  "Date": "2026-03-05",
  "License": "GPL-3",
  "Title": "Multi-Modal Single-Cell Analysis Methods",
  "Description": "Assorted utilities for multi-modal analyses of single-cell\ndatasets. Includes functions to combine multiple modalities for\ndownstream analysis, perform MNN-based batch correction across\nmultiple modalities, and to compute correlations between assay\nvalues for different modalities.",
  "VignetteBuilder": "knitr",
  "biocViews": "ImmunoOncology, SingleCell, RNASeq",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "URL": "http://bioconductor.org/packages/mumosa",
  "BugReports": "https://support.bioconductor.org/",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:54:39 UTC",
  "RemoteUrl": "https://github.com/bioc/mumosa",
  "RemoteRef": "HEAD",
  "RemoteSha": "cf328e4af125be67722e2fa4e2a346d55472d3ce",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-13 09:53:04 UTC",
    "User": "root"
  },
  "Author": "Aaron Lun [aut, cre]",
  "Maintainer": "Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>",
  "MD5sum": "5f442b3cfbf67c92c4b36b2e5d508c6b",
  "_user": "bioc",
  "_type": "src",
  "_file": "mumosa_1.21.0.tar.gz",
  "_fileid": "7cc2fba81a6c1c54ac9f85e17361f223ddaa613fe424f485a03d0a04aa2501ac",
  "_filesize": 471223,
  "_sha256": "7cc2fba81a6c1c54ac9f85e17361f223ddaa613fe424f485a03d0a04aa2501ac",
  "_created": "2026-05-13T09:53:04.000Z",
  "_published": "2026-05-22T09:40:14.164Z",
  "_jobs": [
    {
      "job": 77354241591,
      "time": 255,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6967017202"
    },
    {
      "job": 77354241947,
      "time": 498,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "6967105587"
    },
    {
      "job": 77354241729,
      "time": 502,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "6967107349"
    },
    {
      "job": 77354241998,
      "time": 373,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "6967391390"
    },
    {
      "job": 77354241632,
      "time": 360,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "6967056716"
    },
    {
      "job": 77354241370,
      "time": 375,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6966923614"
    },
    {
      "job": 77354241103,
      "time": 223,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7157477314"
    },
    {
      "job": 77354241851,
      "time": 1063,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "6967298300"
    },
    {
      "job": 77354242070,
      "time": 881,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "6967238213"
    },
    {
      "job": 77354241640,
      "time": 853,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "6967228615"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25791434688",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/mumosa",
  "_commit": {
    "id": "cf328e4af125be67722e2fa4e2a346d55472d3ce",
    "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": 1777380879
  },
  "_maintainer": {
    "name": "Aaron Lun",
    "email": "infinite.monkeys.with.keyboards@gmail.com",
    "login": "ltla",
    "twitter": "@realAaronLun",
    "uuid": 8166669
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "SingleCellExperiment",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "DelayedArray",
      "role": "Imports"
    },
    {
      "package": "DelayedMatrixStats",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "BiocNeighbors",
      "role": "Imports"
    },
    {
      "package": "BiocSingular",
      "role": "Imports"
    },
    {
      "package": "ScaledMatrix",
      "role": "Imports"
    },
    {
      "package": "beachmat",
      "role": "Imports"
    },
    {
      "package": "scuttle",
      "role": "Imports"
    },
    {
      "package": "metapod",
      "role": "Imports"
    },
    {
      "package": "scran",
      "role": "Imports"
    },
    {
      "package": "batchelor",
      "role": "Imports"
    },
    {
      "package": "uwot",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "scater",
      "role": "Suggests"
    },
    {
      "package": "bluster",
      "role": "Suggests"
    },
    {
      "package": "DropletUtils",
      "role": "Suggests"
    },
    {
      "package": "scRNAseq",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-10",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.21.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.20.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "singlecell",
    "rnaseq"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 358,
    "source": "https://www.bioconductor.org/packages/stats/bioc/mumosa"
  },
  "_searchresults": 18,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/mumosa.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "calculateMultiUMAP",
    "computeCorrelations",
    "findTopCorrelations",
    "intersectClusters",
    "intersectGraphs",
    "multiModalMNN",
    "rescaleByNeighbors",
    "runMultiUMAP"
  ],
  "_help": [
    {
      "page": "computeCorrelations",
      "title": "Compute correlations between modes",
      "topics": [
        "computeCorrelations",
        "computeCorrelations,ANY-method",
        "computeCorrelations,SummarizedExperiment-method"
      ]
    },
    {
      "page": "findTopCorrelations",
      "title": "Find top correlations between features",
      "topics": [
        "findTopCorrelations",
        "findTopCorrelations,ANY-method",
        "findTopCorrelations,SummarizedExperiment-method"
      ]
    },
    {
      "page": "intersectClusters",
      "title": "Intersect pre-defined clusters",
      "topics": [
        "intersectClusters"
      ]
    },
    {
      "page": "intersectGraphs",
      "title": "Intersect two graphs",
      "topics": [
        "intersectGraphs"
      ]
    },
    {
      "page": "multiModalMNN",
      "title": "Multi-modal batch correction with MNNs",
      "topics": [
        "multiModalMNN"
      ]
    },
    {
      "page": "rescaleByNeighbors",
      "title": "Rescale matrices for different modes",
      "topics": [
        "rescaleByNeighbors",
        "rescaleByNeighbors,ANY-method",
        "rescaleByNeighbors,SingleCellExperiment-method",
        "rescaleByNeighbors,SummarizedExperiment-method"
      ]
    },
    {
      "page": "runMultiUMAP",
      "title": "Multi-modal UMAP",
      "topics": [
        "calculateMultiUMAP",
        "calculateMultiUMAP,ANY-method",
        "calculateMultiUMAP,SingleCellExperiment-method",
        "calculateMultiUMAP,SummarizedExperiment-method",
        "runMultiUMAP"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/mumosa/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "assorthead",
    "batchelor",
    "beachmat",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocNeighbors",
    "BiocParallel",
    "BiocSingular",
    "bluster",
    "cli",
    "cluster",
    "codetools",
    "cpp11",
    "DelayedArray",
    "DelayedMatrixStats",
    "dqrng",
    "edgeR",
    "FNN",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "glue",
    "igraph",
    "IRanges",
    "irlba",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "metapod",
    "pkgconfig",
    "Rcpp",
    "RcppAnnoy",
    "RcppEigen",
    "RcppProgress",
    "ResidualMatrix",
    "rlang",
    "RSpectra",
    "rsvd",
    "S4Arrays",
    "S4Vectors",
    "ScaledMatrix",
    "scran",
    "scuttle",
    "Seqinfo",
    "SingleCellExperiment",
    "sitmo",
    "snow",
    "SparseArray",
    "sparseMatrixStats",
    "statmod",
    "SummarizedExperiment",
    "uwot",
    "vctrs",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "overview.Rmd",
      "filename": "overview.html",
      "title": "Utilities for multi-modal single-cell analyses",
      "author": "Aaron Lun",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Setting up the dataset",
        "Rescaling by neighbors",
        "Intersecting clusters",
        "Multi-metric UMAP",
        "Intersecting graphs",
        "Correlation analyses",
        "Session information"
      ],
      "created": "2020-11-30 06:25:23",
      "modified": "2024-03-05 23:12:36",
      "commits": 7
    }
  ],
  "_score": 4.431363764158988,
  "_indexed": true,
  "_nocasepkg": "mumosa",
  "_universes": [
    "bioc",
    "ltla"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.21.0",
      "date": "2026-05-13T09:57:43.000Z",
      "distro": "noble",
      "commit": "cf328e4af125be67722e2fa4e2a346d55472d3ce",
      "fileid": "1871003e09c486ec0581dbd2a5c549497127df24c85fbd8b61293b2133406ab6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25791434688"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.21.0",
      "date": "2026-05-13T09:58:03.000Z",
      "distro": "noble",
      "commit": "cf328e4af125be67722e2fa4e2a346d55472d3ce",
      "fileid": "26980b69db2cc943c1a47e9063fc463fc15a4143928f03c38b7671e33b352079",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25791434688"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.21.0",
      "date": "2026-05-13T10:12:11.000Z",
      "commit": "cf328e4af125be67722e2fa4e2a346d55472d3ce",
      "fileid": "2570687d60ef7811318edec2c89f931641ec3d23e2554f7cd0ae30a89c428c07",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25791434688"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.21.0",
      "date": "2026-05-13T09:56:23.000Z",
      "commit": "cf328e4af125be67722e2fa4e2a346d55472d3ce",
      "fileid": "dfd182638e6b0f9f4b27dafcb574ea5bf28eafc21d39b14688b064c2502e2820",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25791434688"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.21.0",
      "date": "2026-05-13T10:06:05.000Z",
      "commit": "cf328e4af125be67722e2fa4e2a346d55472d3ce",
      "fileid": "5f6e8cf71ca62b3ecb5875b72a8a71c1bceace1063ed2a76dbdc04913d62a32f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25791434688"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.21.0",
      "date": "2026-05-13T10:04:23.000Z",
      "commit": "cf328e4af125be67722e2fa4e2a346d55472d3ce",
      "fileid": "d752ba653d6eaf80a62b649e5f6e7bf6384871a2754c7f80c40b3deee90298e8",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25791434688"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.21.0",
      "date": "2026-05-13T10:03:56.000Z",
      "commit": "cf328e4af125be67722e2fa4e2a346d55472d3ce",
      "fileid": "f19ed99fb1627ddb08d625291ea4a591cbdede916328aa793e52cef74f7ff77e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25791434688"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.21.0",
      "date": "2026-05-22T09:39:45.000Z",
      "commit": "cf328e4af125be67722e2fa4e2a346d55472d3ce",
      "fileid": "7ffc283392eec96d88d33c79c4a8afe72dd1a93cb71a7982cf5c5721e228dc48",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25791434688"
    }
  ]
}