{
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  "Type": "Package",
  "Package": "Spectre",
  "Title": "High-dimensional cytometry and imaging analysis",
  "Version": "1.3.0",
  "Date": "2025-08-22",
  "Authors@R": "c(\nperson(\"Thomas\", \"Ashhurst\", , \"thomas.ashhurst@sydney.edu.au\", role = c(\"aut\", \"cre\")),\nperson(\"Felix\", \"Marsh-Wakefield\", , \"felix.marsh-wakefield@sydney.edu.au\", role = \"aut\"),\nperson(\"Givanna\", \"Putri\", , \"putri.g@wehi.edu.au\", role = \"aut\")\n)",
  "Description": "A computational toolkit in R for the integration,\nexploration, and analysis of high-dimensional single-cell\ncytometry and imaging data.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/ImmuneDynamics/Spectre,\nhttp://immunedynamics.io/Spectre/",
  "BugReports": "https://github.com/ImmuneDynamics/Spectre/issues",
  "biocViews": "",
  "Remotes": [
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  "Repository": "https://agshaas.r-universe.dev",
  "Date/Publication": "2025-09-19 00:41:01 UTC",
  "RemoteUrl": "https://github.com/immunedynamics/spectre",
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  "Packaged": {
    "Date": "2026-10-04 14:44:37 UTC",
    "User": "root"
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  "Author": "Thomas Ashhurst [aut, cre],\nFelix Marsh-Wakefield [aut],\nGivanna Putri [aut]",
  "Maintainer": "Thomas Ashhurst <thomas.ashhurst@sydney.edu.au>",
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    "followers": 5,
    "description": "Hi! We are the Haas lab at the Berlin Institute of Health at Charité - Universitätsmedizin Berlin and the MDC-BIMSB."
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    "adjust.files",
    "check.files",
    "create.dt",
    "create.stats",
    "create.sumtable",
    "do.add.cols",
    "do.add.masks",
    "do.add.percell",
    "do.aggregate",
    "do.align",
    "do.asinh",
    "do.calculate.area",
    "do.clip",
    "do.combine.cols",
    "do.create.outlines",
    "do.extract",
    "do.extract.cell.dat",
    "do.filter",
    "do.filter.percell",
    "do.label.from.polygon",
    "do.list.summary",
    "do.list.switch",
    "do.logicle",
    "do.merge.files",
    "do.pull.data",
    "do.reorder",
    "do.rescale",
    "do.stats",
    "do.subsample",
    "do.zscore",
    "fast.colour.plot",
    "fast.multi.plot",
    "make.autograph",
    "make.colour.plot",
    "make.multi.plot",
    "make.pheatmap",
    "make.spatial.plot",
    "make.volcano.plot",
    "package.check",
    "package.install",
    "package.load",
    "prep.cytonorm",
    "read.files",
    "read.spatial.files",
    "run.align",
    "run.cytonorm",
    "run.fitsne",
    "run.flowsom",
    "run.harmony",
    "run.knn.classifier",
    "run.pca",
    "run.phenograph",
    "run.rpca",
    "run.spatial.analysis",
    "run.tsne",
    "run.umap",
    "spatial",
    "train.cytonorm",
    "train.knn.classifier",
    "write.files",
    "write.hdf5"
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  "_datasets": [
    {
      "name": "demo.clustered",
      "title": "demo.clustered - Demo data.table with cells (rows) x markers (columns), with clusters, populations, and UMAP values added",
      "object": "demo.clustered",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "FileName",
        "NK11",
        "CD3",
        "CD45",
        "Ly6G",
        "CD11b",
        "B220",
        "CD8a",
        "Ly6C",
        "CD4",
        "NK11_asinh",
        "CD3_asinh",
        "CD45_asinh",
        "Ly6G_asinh",
        "CD11b_asinh",
        "B220_asinh",
        "CD8a_asinh",
        "Ly6C_asinh",
        "CD4_asinh",
        "Sample",
        "Group",
        "Batch",
        "FlowSOM_cluster",
        "FlowSOM_metacluster",
        "Population",
        "UMAP_X",
        "UMAP_Y"
      ],
      "rows": 169004,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "adjust.files",
      "title": "adjust.files",
      "topics": [
        "adjust.files"
      ]
    },
    {
      "page": "check.files",
      "title": "check.files",
      "topics": [
        "check.files"
      ]
    },
    {
      "page": "create.dt",
      "title": "create.dt - convert a Seurat or SingleCellExperiment to a data.table",
      "topics": [
        "create.dt"
      ]
    },
    {
      "page": "create.stats",
      "title": "create.stats - perform statistical analysis and generate an output data.table",
      "topics": [
        "create.stats"
      ]
    },
    {
      "page": "create.sumtable",
      "title": "create.sumtable - create a data.table 'summarising' cellular data by sample and population/cluster.",
      "topics": [
        "create.sumtable"
      ]
    },
    {
      "page": "demo.clustered",
      "title": "demo.clustered - Demo data.table with cells (rows) x markers (columns), with clusters, populations, and UMAP values added",
      "topics": [
        "demo.clustered"
      ]
    },
    {
      "page": "do.add.cols",
      "title": "do.add.cols",
      "topics": [
        "do.add.cols"
      ]
    },
    {
      "page": "do.add.masks",
      "title": "do.add.masks",
      "topics": [
        "do.add.masks"
      ]
    },
    {
      "page": "do.add.percell",
      "title": "do.add.percell",
      "topics": [
        "do.add.percell"
      ]
    },
    {
      "page": "do.aggregate",
      "title": "Aggregate data using data.table functions - summarises the mean, median, or sum expression of each marker on each cluster/population",
      "topics": [
        "do.aggregate"
      ]
    },
    {
      "page": "do.align",
      "title": "do.align - Function to align multiple batches of a dataset.",
      "topics": [
        "do.align"
      ]
    },
    {
      "page": "do.asinh",
      "title": "Transform data using ArcSinh transformation",
      "topics": [
        "do.asinh"
      ]
    },
    {
      "page": "do.calculate.area",
      "title": "do.calculate.area",
      "topics": [
        "do.calculate.area"
      ]
    },
    {
      "page": "do.clip",
      "title": "do.clip - Clips data using a specified lower and upper value",
      "topics": [
        "do.clip"
      ]
    },
    {
      "page": "do.combine.cols",
      "title": "do.combine.cols - Combine the values of two columns into a single column",
      "topics": [
        "do.combine.cols"
      ]
    },
    {
      "page": "do.create.outlines",
      "title": "do.create.outlines",
      "topics": [
        "do.create.outlines"
      ]
    },
    {
      "page": "do.extract",
      "title": "do.extract",
      "topics": [
        "do.extract"
      ]
    },
    {
      "page": "do.extract.cell.dat",
      "title": "do.extract.cell.dat",
      "topics": [
        "do.extract.cell.dat"
      ]
    },
    {
      "page": "do.filter",
      "title": "do.filter - filtering data.table using multiple match values",
      "topics": [
        "do.filter"
      ]
    },
    {
      "page": "do.filter.percell",
      "title": "do.filter.percell",
      "topics": [
        "do.filter.percell"
      ]
    },
    {
      "page": "do.label.from.polygon",
      "title": "do.label.from.polygon",
      "topics": [
        "do.label.from.polygon"
      ]
    },
    {
      "page": "do.list.summary",
      "title": "Summarise the column names and row numbers for elements of a list",
      "topics": [
        "do.list.summary"
      ]
    },
    {
      "page": "do.list.switch",
      "title": "List switch or inversion",
      "topics": [
        "do.list.switch"
      ]
    },
    {
      "page": "do.logicle",
      "title": "Using logicle to transform data",
      "topics": [
        "do.logicle"
      ]
    },
    {
      "page": "do.merge.files",
      "title": "do.merge.files - Function to merge a list of data.tables (one data.table per 'sample') into a single large data.table.",
      "topics": [
        "do.merge.files"
      ]
    },
    {
      "page": "do.pull.data",
      "title": "do.pull.data",
      "topics": [
        "do.pull.data"
      ]
    },
    {
      "page": "do.reorder",
      "title": "do.reorder - custom row re-ordering of a data.table",
      "topics": [
        "do.reorder"
      ]
    },
    {
      "page": "do.rescale",
      "title": "do.rescale - Re-scale data in selected columns between two values, usually 0 and 1.",
      "topics": [
        "do.rescale"
      ]
    },
    {
      "page": "do.stats",
      "title": "Statistical analysis",
      "topics": [
        "do.stats"
      ]
    },
    {
      "page": "do.subsample",
      "title": "Subsample data",
      "topics": [
        "do.subsample"
      ]
    },
    {
      "page": "do.zscore",
      "title": "do.zscore - Calculate z.score for a dataset",
      "topics": [
        "do.zscore"
      ]
    },
    {
      "page": "fast.colour.plot",
      "title": "DEPRECATED fast colour plot",
      "topics": [
        "fast.colour.plot"
      ]
    },
    {
      "page": "fast.multi.plot",
      "title": "DEPRECATED fast multi plot",
      "topics": [
        "fast.multi.plot"
      ]
    },
    {
      "page": "make.autograph",
      "title": "make.autograph - Creates plots using ggplot2",
      "topics": [
        "make.autograph"
      ]
    },
    {
      "page": "make.colour.plot",
      "title": "Make colour plot",
      "topics": [
        "make.colour.plot"
      ]
    },
    {
      "page": "make.multi.plot",
      "title": "Make multiple plots for multiple columns and/or multiple sample/group/clusters",
      "topics": [
        "make.multi.plot"
      ]
    },
    {
      "page": "make.pheatmap",
      "title": "make.pheatmap - Create a 'pretty' heatmap (pheatmap)",
      "topics": [
        "make.pheatmap"
      ]
    },
    {
      "page": "make.spatial.plot",
      "title": "make.spatial.plot",
      "topics": [
        "make.spatial.plot"
      ]
    },
    {
      "page": "make.volcano.plot",
      "title": "Make an enhanced volcano plot",
      "topics": [
        "make.volcano.plot"
      ]
    },
    {
      "page": "package.check",
      "title": "package.check - a function to check the installation of all required packages.",
      "topics": [
        "package.check"
      ]
    },
    {
      "page": "package.install",
      "title": "package.install - a function to install packages required for Spectre.",
      "topics": [
        "package.install"
      ]
    },
    {
      "page": "package.load",
      "title": "package.load - a function to load (library) all required packages.",
      "topics": [
        "package.load"
      ]
    },
    {
      "page": "prep.cytonorm",
      "title": "prep.cytonorm - Prepare reference data into a FlowSOM object",
      "topics": [
        "prep.cytonorm"
      ]
    },
    {
      "page": "read.files",
      "title": "Read CSV or FCS files into a list.",
      "topics": [
        "read.files"
      ]
    },
    {
      "page": "read.spatial.files",
      "title": "Read TIFF files into R and and create spatial data object",
      "topics": [
        "read.spatial.files"
      ]
    },
    {
      "page": "run.align",
      "title": "run.align - Run the alignment model on a target data.table",
      "topics": [
        "run.align"
      ]
    },
    {
      "page": "run.cytonorm",
      "title": "run.cytonorm - Run the alignment model on a target data.table",
      "topics": [
        "run.cytonorm"
      ]
    },
    {
      "page": "run.fitsne",
      "title": "Run FIt-SNE, Fourier Transform TSNE.",
      "topics": [
        "run.fitsne"
      ]
    },
    {
      "page": "run.flowsom",
      "title": "Run FlowSOM",
      "topics": [
        "run.flowsom"
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