{
  "_id": "6a153c43acfb0bcc41d531fc",
  "Package": "CATALYST",
  "Type": "Package",
  "Title": "Cytometry dATa anALYSis Tools",
  "Version": "1.37.0",
  "Authors@R": "c(\nperson(\"Helena L.\", \"Crowell\",\nrole=c(\"aut\", \"cre\"),\nemail=\"helena@crowell.eu\",\ncomment=c(ORCID=\"0000-0002-4801-1767\")),\nperson(\"Vito R.T.\", \"Zanotelli\", role=\"aut\",\ncomment=c(ORCID=\"0000-0001-7268-311X\")),\nperson(\"Stéphane\", \"Chevrier\", role=c(\"aut\", \"dtc\"),\ncomment=c(ORCID=\"0000-0002-9216-7910\")),\nperson(\"Mark D.\", \"Robinson\", role=c(\"aut\", \"fnd\"),\ncomment=c(ORCID=\"0000-0002-3048-5518\")),\nperson(\"Bernd\", \"Bodenmiller\", role=\"fnd\",\ncomment=c(ORCID=\"0000-0002-6325-7861\")))",
  "biocViews": "Clustering, DataImport, DifferentialExpression,\nExperimentalDesign, FlowCytometry, ImmunoOncology,\nMassSpectrometry,Normalization, Preprocessing, SingleCell,\nSoftware, StatisticalMethod, Visualization",
  "Description": "CATALYST provides tools for preprocessing of and\ndifferential discovery in cytometry data such as FACS, CyTOF,\nand IMC. Preprocessing includes i) normalization using bead\nstandards, ii) single-cell deconvolution, and iii) bead-based\ncompensation. For differential discovery, the package provides\na number of convenient functions for data processing (e.g.,\nclustering, dimension reduction), as well as a suite of\nvisualizations for exploratory data analysis and exploration of\nresults from differential abundance (DA) and state (DS)\nanalysis in order to identify differences in composition and\nexpression profiles at the subpopulation-level, respectively.",
  "URL": "https://github.com/HelenaLC/CATALYST",
  "BugReports": "https://github.com/HelenaLC/CATALYST/issues",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.3",
  "License": "GPL (>=2)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libglpk-dev make\nlibharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev\nlibwebp-dev libxml2-dev libssl-dev perl zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:45:30 UTC",
  "RemoteUrl": "https://github.com/bioc/CATALYST",
  "RemoteRef": "HEAD",
  "RemoteSha": "4740c0e4b1ae65601eb0fd8f8820c39919952d77",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-26 06:10:04 UTC",
    "User": "root"
  },
  "Author": "Helena L. Crowell [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-4801-1767>),\nVito R.T. Zanotelli [aut] (ORCID:\n<https://orcid.org/0000-0001-7268-311X>),\nStéphane Chevrier [aut, dtc] (ORCID:\n<https://orcid.org/0000-0002-9216-7910>),\nMark D. Robinson [aut, fnd] (ORCID:\n<https://orcid.org/0000-0002-3048-5518>),\nBernd Bodenmiller [fnd] (ORCID:\n<https://orcid.org/0000-0002-6325-7861>)",
  "Maintainer": "Helena L. Crowell <helena@crowell.eu>",
  "MD5sum": "a7a44079cc663a1bd384ef4ba379c1dc",
  "_user": "bioc",
  "_type": "src",
  "_file": "CATALYST_1.37.0.tar.gz",
  "_fileid": "a8fea7f9c1bffcc99acd1cc4432200000a4561f2450733496cf127376e887981",
  "_filesize": 11701032,
  "_sha256": "a8fea7f9c1bffcc99acd1cc4432200000a4561f2450733496cf127376e887981",
  "_created": "2026-05-26T06:10:04.000Z",
  "_published": "2026-05-26T06:22:59.637Z",
  "_jobs": [
    {
      "job": 77817514050,
      "time": 262,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7210116263"
    },
    {
      "job": 77817514158,
      "time": 693,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7210210072"
    },
    {
      "job": 77817514060,
      "time": 668,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7210204161"
    },
    {
      "job": 77817514137,
      "time": 310,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7210141522"
    },
    {
      "job": 77817514072,
      "time": 404,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7210157506"
    },
    {
      "job": 77816744641,
      "time": 416,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7210059587"
    },
    {
      "job": 77817514119,
      "time": 205,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7210104163"
    },
    {
      "job": 77817514173,
      "time": 608,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7210191390"
    },
    {
      "job": 77817514175,
      "time": 599,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7210189494"
    },
    {
      "job": 77817514170,
      "time": 556,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7210179591"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 9
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26435319239",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/CATALYST",
  "_commit": {
    "id": "4740c0e4b1ae65601eb0fd8f8820c39919952d77",
    "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": 1777380330
  },
  "_maintainer": {
    "name": "Helena L. Crowell",
    "email": "helena@crowell.eu",
    "login": "helenalc",
    "description": "",
    "uuid": 14542264,
    "orcid": "0000-0002-4801-1767"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5",
      "role": "Depends"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Depends"
    },
    {
      "package": "circlize",
      "role": "Imports"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Imports"
    },
    {
      "package": "ConsensusClusterPlus",
      "role": "Imports"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "drc",
      "role": "Imports"
    },
    {
      "package": "flowCore",
      "role": "Imports"
    },
    {
      "package": "FlowSOM",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "ggridges",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "nnls",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "Rtsne",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "scater",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "diffcyt",
      "role": "Suggests"
    },
    {
      "package": "flowWorkspace",
      "role": "Suggests"
    },
    {
      "package": "ggcyto",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "openCyto",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "uwot",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2025-28",
      "n": 1
    },
    {
      "week": "2025-38",
      "n": 1
    },
    {
      "week": "2025-40",
      "n": 6
    },
    {
      "week": "2025-44",
      "n": 1
    },
    {
      "week": "2025-47",
      "n": 1
    },
    {
      "week": "2026-11",
      "n": 5
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.37.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.36.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "clustering",
    "dataimport",
    "differentialexpression",
    "experimentaldesign",
    "flowcytometry",
    "immunooncology",
    "massspectrometry",
    "normalization",
    "preprocessing",
    "singlecell",
    "software",
    "statisticalmethod",
    "visualization"
  ],
  "_stars": 75,
  "_contributors": [
    {
      "user": "catalyst-project",
      "count": 1946,
      "uuid": 31732326
    },
    {
      "user": "helenalc",
      "count": 31,
      "uuid": 14542264
    },
    {
      "user": "jwokaty",
      "count": 15,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "hpages",
      "count": 4,
      "uuid": 8810451
    },
    {
      "user": "kayla-morrell",
      "count": 2,
      "uuid": 32339524
    },
    {
      "user": "lmweber",
      "count": 2,
      "uuid": 8062417
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 1124,
    "source": "https://www.bioconductor.org/packages/stats/bioc/CATALYST"
  },
  "_mentions": 37,
  "_devurl": "https://github.com/helenalc/catalyst",
  "_searchresults": 504,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/CATALYST.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/helenalc/catalyst",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "adaptSpillmat",
    "applyCutoffs",
    "assignPrelim",
    "channels",
    "clrDR",
    "cluster",
    "cluster_codes",
    "cluster_ids",
    "compCytof",
    "computeSpillmat",
    "delta_area",
    "ei",
    "estCutoffs",
    "extractClusters",
    "filterSCE",
    "guessPanel",
    "marker_classes",
    "mergeClusters",
    "n_cells",
    "normCytof",
    "pbMDS",
    "plotAbundances",
    "plotClusterExprs",
    "plotCodes",
    "plotCounts",
    "plotDiffHeatmap",
    "plotDR",
    "plotEvents",
    "plotExprHeatmap",
    "plotExprs",
    "plotFreqHeatmap",
    "plotMahal",
    "plotMultiHeatmap",
    "plotNRS",
    "plotPbExprs",
    "plotScatter",
    "plotSpillmat",
    "plotYields",
    "prepData",
    "runDR",
    "sample_ids",
    "sce2fcs",
    "state_markers",
    "type_markers"
  ],
  "_datasets": [
    {
      "name": "isotope_list",
      "title": "Example data sets",
      "object": "isotope_list",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "merging_table",
      "title": "Example data sets",
      "object": "merging_table",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "old_cluster",
        "new_cluster"
      ],
      "rows": 20,
      "table": true,
      "tojson": true
    },
    {
      "name": "mp_cells",
      "title": "Example data sets",
      "object": "mp_cells",
      "class": [
        "flowFrame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "PBMC_fs",
      "title": "Example data sets",
      "object": "PBMC_fs",
      "class": [
        "flowSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "PBMC_md",
      "title": "Example data sets",
      "object": "PBMC_md",
      "class": [
        "data.frame"
      ],
      "fields": [
        "file_name",
        "sample_id",
        "condition",
        "patient_id"
      ],
      "rows": 8,
      "table": true,
      "tojson": true
    },
    {
      "name": "PBMC_panel",
      "title": "Example data sets",
      "object": "PBMC_panel",
      "class": [
        "data.frame"
      ],
      "fields": [
        "fcs_colname",
        "antigen",
        "marker_class"
      ],
      "rows": 24,
      "table": true,
      "tojson": true
    },
    {
      "name": "raw_data",
      "title": "Example data sets",
      "object": "raw_data",
      "class": [
        "flowSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sample_ff",
      "title": "Example data sets",
      "object": "sample_ff",
      "class": [
        "flowFrame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sample_key",
      "title": "Example data sets",
      "object": "sample_key",
      "class": [
        "data.frame"
      ],
      "fields": [
        "102",
        "104",
        "105",
        "106",
        "108",
        "110"
      ],
      "rows": 20,
      "table": true,
      "tojson": true
    },
    {
      "name": "ss_exp",
      "title": "Example data sets",
      "object": "ss_exp",
      "class": [
        "flowFrame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "adaptSpillmat",
      "title": "Adapt spillover matrix",
      "topics": [
        "adaptSpillmat"
      ]
    },
    {
      "page": "applyCutoffs",
      "title": "Single-cell debarcoding (2)",
      "topics": [
        "applyCutoffs"
      ]
    },
    {
      "page": "assignPrelim",
      "title": "Single-cell debarcoding (1)",
      "topics": [
        "assignPrelim"
      ]
    },
    {
      "page": "clrDR",
      "title": "DR plot on CLR of proportions",
      "topics": [
        "clrDR"
      ]
    },
    {
      "page": "cluster",
      "title": "'FlowSOM' clustering & 'ConsensusClusterPlus' metaclustering",
      "topics": [
        "cluster"
      ]
    },
    {
      "page": "compCytof",
      "title": "Compensate CyTOF data",
      "topics": [
        "compCytof"
      ]
    },
    {
      "page": "computeSpillmat",
      "title": "Compute spillover matrix",
      "topics": [
        "computeSpillmat"
      ]
    },
    {
      "page": "data",
      "title": "Example data sets",
      "topics": [
        "data",
        "isotope_list",
        "merging_table",
        "mp_cells",
        "PBMC_fs",
        "PBMC_md",
        "PBMC_panel",
        "raw_data",
        "sample_ff",
        "sample_key",
        "ss_exp"
      ]
    },
    {
      "page": "estCutoffs",
      "title": "Estimation of distance separation cutoffs",
      "topics": [
        "estCutoffs"
      ]
    },
    {
      "page": "extractClusters",
      "title": "Extract clusters from a 'SingleCellExperiment'",
      "topics": [
        "extractClusters"
      ]
    },
    {
      "page": "filterSCE",
      "title": "'SingleCellExperiment' filtering",
      "topics": [
        "filterSCE"
      ]
    },
    {
      "page": "guessPanel",
      "title": "Guess parameter panel",
      "topics": [
        "guessPanel"
      ]
    },
    {
      "page": "mergeClusters",
      "title": "Manual cluster merging",
      "topics": [
        "mergeClusters"
      ]
    },
    {
      "page": "normCytof",
      "title": "Bead-based normalization",
      "topics": [
        "normCytof"
      ]
    },
    {
      "page": "pbMDS",
      "title": "Pseudobulk-level MDS plot",
      "topics": [
        "pbMDS"
      ]
    },
    {
      "page": "plotAbundances",
      "title": "Population frequencies across samples & clusters",
      "topics": [
        "plotAbundances"
      ]
    },
    {
      "page": "plotClusterExprs",
      "title": "Plot expression distributions by cluster",
      "topics": [
        "plotClusterExprs"
      ]
    },
    {
      "page": "plotCodes",
      "title": "tSNE and PCA on SOM codes",
      "topics": [
        "plotCodes"
      ]
    },
    {
      "page": "plotCounts",
      "title": "Plot cell counts",
      "topics": [
        "plotCounts"
      ]
    },
    {
      "page": "plotDiffHeatmap",
      "title": "Plot differential heatmap",
      "topics": [
        "plotDiffHeatmap"
      ]
    },
    {
      "page": "plotDR",
      "title": "Plot reduced dimensions",
      "topics": [
        "plotDR"
      ]
    },
    {
      "page": "plotEvents",
      "title": "Event plot",
      "topics": [
        "plotEvents"
      ]
    },
    {
      "page": "plotExprHeatmap",
      "title": "Plot expression heatmap",
      "topics": [
        "plotExprHeatmap"
      ]
    },
    {
      "page": "plotExprs",
      "title": "Expression densities",
      "topics": [
        "plotExprs"
      ]
    },
    {
      "page": "plotFreqHeatmap",
      "title": "Cluster frequency heatmap",
      "topics": [
        "plotFreqHeatmap"
      ]
    },
    {
      "page": "plotMahal",
      "title": "Biaxial plot",
      "topics": [
        "plotMahal"
      ]
    },
    {
      "page": "plotMultiHeatmap",
      "title": "Multi-panel expression & frequency heatmaps",
      "topics": [
        "plotMultiHeatmap"
      ]
    },
    {
      "page": "plotNRS",
      "title": "Plot non-redundancy scores",
      "topics": [
        "plotNRS"
      ]
    },
    {
      "page": "plotPbExprs",
      "title": "Pseudobulk-level boxplot",
      "topics": [
        "plotPbExprs"
      ]
    },
    {
      "page": "plotScatter",
      "title": "Scatter plot",
      "topics": [
        "plotScatter"
      ]
    },
    {
      "page": "plotSpillmat",
      "title": "Spillover matrix heatmap",
      "topics": [
        "plotSpillmat"
      ]
    },
    {
      "page": "plotYields",
      "title": "Yield plot",
      "topics": [
        "plotYields"
      ]
    },
    {
      "page": "prepData",
      "title": "Data preparation",
      "topics": [
        "prepData"
      ]
    },
    {
      "page": "runDR",
      "title": "Dimension reduction",
      "topics": [
        "runDR"
      ]
    },
    {
      "page": "SCE-accessors",
      "title": "'SingleCellExperiment' accessors",
      "topics": [
        "channels",
        "channels,SingleCellExperiment-method",
        "cluster_codes",
        "cluster_codes,SingleCellExperiment-method",
        "cluster_ids",
        "cluster_ids,SingleCellExperiment,character-method",
        "cluster_ids,SingleCellExperiment,missing-method",
        "delta_area",
        "delta_area,SingleCellExperiment-method",
        "ei",
        "ei,SingleCellExperiment-method",
        "marker_classes",
        "marker_classes,SingleCellExperiment-method",
        "n_cells",
        "n_cells,SingleCellExperiment-method",
        "sample_ids",
        "sample_ids,SingleCellExperiment-method",
        "SCE-accessors",
        "state_markers",
        "state_markers,SingleCellExperiment-method",
        "type_markers",
        "type_markers,SingleCellExperiment-method"
      ]
    },
    {
      "page": "sce2fcs",
      "title": "SCE to 'flowFrame/Set'",
      "topics": [
        "sce2fcs"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/CATALYST/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "ALL",
    "assorthead",
    "backports",
    "base64enc",
    "beachmat",
    "beeswarm",
    "BH",
    "Biobase",
    "BiocGenerics",
    "biocmake",
    "BiocNeighbors",
    "BiocParallel",
    "BiocSingular",
    "boot",
    "broom",
    "Cairo",
    "car",
    "carData",
    "circlize",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "colorRamps",
    "colorspace",
    "ComplexHeatmap",
    "ConsensusClusterPlus",
    "corrplot",
    "cowplot",
    "cpp11",
    "crayon",
    "cytolib",
    "DelayedArray",
    "Deriv",
    "digest",
    "dir.expiry",
    "doBy",
    "doParallel",
    "dplyr",
    "dqrng",
    "drc",
    "farver",
    "filelock",
    "flowCore",
    "FlowSOM",
    "FNN",
    "foreach",
    "forecast",
    "formatR",
    "Formula",
    "fracdiff",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "GetoptLong",
    "ggbeeswarm",
    "ggforce",
    "ggnewscale",
    "ggplot2",
    "ggpubr",
    "ggrastr",
    "ggrepel",
    "ggridges",
    "ggsci",
    "ggsignif",
    "GlobalOptions",
    "glue",
    "gridExtra",
    "gtable",
    "gtools",
    "igraph",
    "IRanges",
    "irlba",
    "isoband",
    "iterators",
    "jsonlite",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "mgcv",
    "microbenchmark",
    "minqa",
    "modelr",
    "multcomp",
    "mvtnorm",
    "nlme",
    "nloptr",
    "nnet",
    "nnls",
    "numDeriv",
    "pbkrtest",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "plotrix",
    "plyr",
    "png",
    "polyclip",
    "polynom",
    "purrr",
    "quantreg",
    "R6",
    "ragg",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppAnnoy",
    "RcppArmadillo",
    "RcppEigen",
    "RcppML",
    "RcppProgress",
    "Rdpack",
    "reformulas",
    "reshape2",
    "Rhdf5lib",
    "rjson",
    "rlang",
    "RProtoBufLib",
    "RSpectra",
    "rstatix",
    "rsvd",
    "Rtsne",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sandwich",
    "ScaledMatrix",
    "scales",
    "scater",
    "scuttle",
    "Seqinfo",
    "shape",
    "SingleCellExperiment",
    "sitmo",
    "snow",
    "SparseArray",
    "SparseM",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "systemfonts",
    "textshaping",
    "TH.data",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "tweenr",
    "urca",
    "utf8",
    "uwot",
    "vctrs",
    "vipor",
    "viridis",
    "viridisLite",
    "withr",
    "XML",
    "XVector",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "preprocessing.Rmd",
      "filename": "preprocessing.html",
      "title": "Preprocessing with CATALYST",
      "author": "Helena L Crowell, Vito RT Zanotelli, Stéphane Chevrier, Bernd Bodenmiller, Mark D Robinson",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Data examples",
        "Data organization",
        "Normalization",
        "Normalization workflow",
        "normCytof: Normalization using bead standards",
        "Debarcoding",
        "Debarcoding workflow",
        "assignPrelim: Assignment of preliminary IDs",
        "estCutoffs: Estimation of separation cutoffs",
        "plotYields: Selecting barcode separation cutoffs",
        "applyCutoffs: Applying deconvolution parameters",
        "plotEvents: Normalized intensities",
        "plotMahal: All barcode biaxial plot",
        "Compensation",
        "Compensation workflow",
        "computeSpillmat: Estimation of the spillover matrix",
        "plotSpillmat: Spillover matrix heatmap",
        "compCytof: Compensation of mass cytometry data",
        "Scatter plot visualization",
        "Example 1: Coloring by cell density",
        "Example 2: Coloring by variables",
        "Example 3: Facetting by variables",
        "Conversion to other data structures",
        "Writing FCS files",
        "Gating & visualization",
        "Session information",
        "References"
      ],
      "created": "2018-05-13 08:15:30",
      "modified": "2025-10-05 20:09:59",
      "commits": 11
    },
    {
      "source": "differential.Rmd",
      "filename": "differential.html",
      "title": "Differential discovery with CATALYST",
      "author": "Helena L Crowell, Mark D Robinson",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Example data",
        "Data preparation",
        "Clustering",
        "cluster: FlowSOM clustering & ConsensusClusterPlus metaclustering",
        "mergeClusters: Manual cluster merging",
        "Delta area plot",
        "Visualization",
        "plotCounts: Number of cells measured per sample",
        "pbMDS: Pseudobulk-level MDS plot",
        "Ex. 2: MDS on sample-level pseudobulks",
        "Ex. 1: MDS on pseudobulks by cluster-sample",
        "clrDR: Reduced dimension plot on CLR of proportions",
        "Ex. 1: CLR on cluster proportions across samples",
        "Ex. 2: CLR on sample proportions across clusters",
        "plotExprHeatmap: Heatmap of aggregated marker expressions",
        "plotPbExprs: Pseudobulk expression boxplot",
        "plotClusterExprs: Marker-densities by cluster",
        "plotAbundances: Relative population abundances",
        "plotFreqHeatmap: Heatmap of cluster fequencies",
        "plotMultiHeatmap: Multi-panel Heatmaps",
        "Ex. 1: Type- & state-markers",
        "Ex. 2: CDx markers & cluster frequencies",
        "Ex. 3: Selected markers",
        "Dimensionality reduction",
        "Filtering",
        "Differental testing with r BiocStyle::Biocpkg(\"diffcyt\")",
        "plotDiffHeatmap: Heatmap of differential testing results",
        "Ex. 1: DA testing results",
        "Ex. 2: DS testing results",
        "Ex. 3: Filtering results",
        "Ex. 4: Customizing appearance",
        "More",
        "Exporting FCS files",
        "Using other clustering algorithms",
        "Customizing visualizations",
        "Modifying ggplots",
        "Modifying ComplexHeatmaps",
        "Combining ComplexHeatmaps",
        "Ex. 1: type- & state-markers + cluster frequencies",
        "Ex. 2: frequencies + selected markers + all markers",
        "Session information",
        "References"
      ],
      "created": "2020-04-14 16:46:21",
      "modified": "2025-10-05 19:45:05",
      "commits": 13
    }
  ],
  "_score": 11.096605441482424,
  "_indexed": true,
  "_nocasepkg": "catalyst",
  "_universes": [
    "bioc",
    "helenalc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.37.0",
      "date": "2026-05-26T06:15:46.000Z",
      "distro": "noble",
      "commit": "4740c0e4b1ae65601eb0fd8f8820c39919952d77",
      "fileid": "5ea0b3487a75caef1e746f4eab849c8918b3c3cecae0a41b4f9813b738447a04",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435319239"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.37.0",
      "date": "2026-05-26T06:15:11.000Z",
      "distro": "noble",
      "commit": "4740c0e4b1ae65601eb0fd8f8820c39919952d77",
      "fileid": "f0309bb0eabdc73e49fb19a445bef2ced440c4abdba46710ce0f2fe2a37fe7f6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435319239"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.37.0",
      "date": "2026-05-26T06:13:33.000Z",
      "commit": "4740c0e4b1ae65601eb0fd8f8820c39919952d77",
      "fileid": "47dc4439e301c5645571d0701e87e5d321eed2214e1959067deaf87bcdd229ca",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435319239"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.37.0",
      "date": "2026-05-26T06:13:41.000Z",
      "commit": "4740c0e4b1ae65601eb0fd8f8820c39919952d77",
      "fileid": "9f353135024ee7159a3ad5181e8f58f2f915f907893e491d95b15210cd5f564b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435319239"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.37.0",
      "date": "2026-05-26T06:14:18.000Z",
      "commit": "4740c0e4b1ae65601eb0fd8f8820c39919952d77",
      "fileid": "080f7e94760a49215b9aa9dc35936d7e027b9a61c3eccb17f37625f25af3978c",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435319239"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-05-26T06:13:13.000Z",
      "commit": "4740c0e4b1ae65601eb0fd8f8820c39919952d77",
      "fileid": "a6fbe5537d0256d1b1823764361b8b2134cd432ffed9c9e7748acc9b7c0e87fd",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435319239"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-05-26T06:13:15.000Z",
      "commit": "4740c0e4b1ae65601eb0fd8f8820c39919952d77",
      "fileid": "642c4ec53995a98f8d011110f0f764d7956b9280435d7e6793b1041fb0b8af0e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435319239"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-05-26T06:12:40.000Z",
      "commit": "4740c0e4b1ae65601eb0fd8f8820c39919952d77",
      "fileid": "efee3da2c0ebe1b86134c863f7d9c2ce83a8a396269466ce4a635b4d41c29fec",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26435319239"
    }
  ]
}