{
  "_id": "6a13f41eacfb0bcc41d3258b",
  "Package": "mumosa",
  "Type": "Package",
  "Authors@R": "person(\"Aaron\", \"Lun\", role = c(\"aut\", \"cre\"), email=\"infinite.monkeys.with.keyboards@gmail.com\")",
  "Version": "1.20.0",
  "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-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:54:39 UTC",
  "RemoteUrl": "https://github.com/bioc/mumosa",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "3761d72ca29b5452b007afea2a6851c314c66b51",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-25 06:44:12 UTC",
    "User": "root"
  },
  "Author": "Aaron Lun [aut, cre]",
  "Maintainer": "Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>",
  "MD5sum": "68368db981bf9b1a51d23ab3e4a2b013",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "mumosa_1.20.0.tar.gz",
  "_fileid": "a0f15e08ed526d0669d3e34f22feb51299b57d7a8503f793e35d0debb40e0be8",
  "_filesize": 470696,
  "_sha256": "a0f15e08ed526d0669d3e34f22feb51299b57d7a8503f793e35d0debb40e0be8",
  "_created": "2026-05-25T06:44:12.000Z",
  "_published": "2026-05-25T07:02:54.158Z",
  "_jobs": [
    {
      "job": 77668702290,
      "time": 266,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7193132207"
    },
    {
      "job": 77668702288,
      "time": 516,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7193187590"
    },
    {
      "job": 77668702304,
      "time": 540,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7193192904"
    },
    {
      "job": 77668702303,
      "time": 241,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7193130916"
    },
    {
      "job": 77668702316,
      "time": 298,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7193141529"
    },
    {
      "job": 77667978264,
      "time": 394,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7193074642"
    },
    {
      "job": 77668702297,
      "time": 209,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7193120191"
    },
    {
      "job": 77668702334,
      "time": 860,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7193264148"
    },
    {
      "job": 77668702314,
      "time": 1067,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7193311909"
    },
    {
      "job": 77668702319,
      "time": 978,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7193290731"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26387090684",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/mumosa",
  "_commit": {
    "id": "3761d72ca29b5452b007afea2a6851c314c66b51",
    "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": 1777380879
  },
  "_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": "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": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-10",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_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": 16,
  "_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/RELEASE_3_23/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": 4.380211241711606,
  "_indexed": false,
  "_nocasepkg": "mumosa",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/mumosa",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.20.0",
      "date": "2026-05-25T06:49:18.000Z",
      "distro": "noble",
      "commit": "3761d72ca29b5452b007afea2a6851c314c66b51",
      "fileid": "2b82a9c8845445a1d2357747e5fd5006a29604e2a9f7f3a17c65e8b9df46839b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26387090684"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.20.0",
      "date": "2026-05-25T06:49:24.000Z",
      "distro": "noble",
      "commit": "3761d72ca29b5452b007afea2a6851c314c66b51",
      "fileid": "3812e7a9390fb413c356463d0d63d8b80b9f193f53a575bfd5a601f848b8e7ec",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26387090684"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.20.0",
      "date": "2026-05-25T06:46:50.000Z",
      "commit": "3761d72ca29b5452b007afea2a6851c314c66b51",
      "fileid": "9babaa669327231ec9182294d9873a9f673d03e8a5bd19559684734443d92a55",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26387090684"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.20.0",
      "date": "2026-05-25T06:47:13.000Z",
      "commit": "3761d72ca29b5452b007afea2a6851c314c66b51",
      "fileid": "e4a7d19e152324e733e29b5806ca5717a678490e11b9f2c1e60cb9b9a884eb47",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26387090684"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.20.0",
      "date": "2026-05-25T06:48:16.000Z",
      "commit": "3761d72ca29b5452b007afea2a6851c314c66b51",
      "fileid": "b078dd27ed6d0b7e12defa99bd32ea96465acd75c94fbcbd34b39d46151fe728",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26387090684"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.20.0",
      "date": "2026-05-25T06:55:05.000Z",
      "commit": "3761d72ca29b5452b007afea2a6851c314c66b51",
      "fileid": "30b9750e9ecce1879ec4d37db40a72c8655227a5a2d0e8b65defbb1b304af8a2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26387090684"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.20.0",
      "date": "2026-05-25T06:58:27.000Z",
      "commit": "3761d72ca29b5452b007afea2a6851c314c66b51",
      "fileid": "0e1dda22b0f6370751ff2cd6eb46834bd03108e499ec5985f03c1c8161fe277f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26387090684"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.20.0",
      "date": "2026-05-25T06:56:12.000Z",
      "commit": "3761d72ca29b5452b007afea2a6851c314c66b51",
      "fileid": "5027e5ac5f5ce9d97d0f9b4276e9865459e2b0668a0ce42bbfad4e76d36ed8cb",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26387090684"
    }
  ]
}