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  "Title": "Analysis of scDNA-seq data",
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  "Description": "Scafari is a Shiny application designed for the analysis\nof single-cell DNA sequencing (scDNA-seq) data provided in .h5\nfile format. The analysis process is structured into the four\nkey steps \"Sequencing\", \"Panel\", \"Variants\", and \"Explore\nVariants\". It supports various analyses and visualizations.",
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  "BugReports": "https://github.com/sophiewind/scafari/issues",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:05:12 UTC",
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  "Author": "Sophie Wind [aut, cre] (ORCID: <https://orcid.org/0009-0002-1174-8201>)",
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    "annotateVariants",
    "clusterVariantSelection",
    "filterVariants",
    "h5ToSce",
    "launchScafariShiny",
    "logLogPlot",
    "normalizeReadCounts",
    "plotAmpliconDistribution",
    "plotClusterGenotype",
    "plotClusterVAF",
    "plotClusterVAFMap",
    "plotElbow",
    "plotGenotypequalityPerGenotype",
    "plotNormalizedReadCounts",
    "plotPanelUniformity",
    "plotVariantHeatmap"
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    {
      "page": "annotateAmplicons",
      "title": "Function: annotateAmplicons This function takes a SingleCellExperiment object as input and annotates the stored amplicons.",
      "topics": [
        "annotateAmplicons"
      ]
    },
    {
      "page": "annotateVariants",
      "title": "Function: annotateVariants This function takes a SingleCellExperiment object as input and performs variant annotation.",
      "topics": [
        "annotateVariants"
      ]
    },
    {
      "page": "clusterVariantSelection",
      "title": "Function: clusterVariantSelection This function takes selected variants and performs clustering on them.",
      "topics": [
        "clusterVariantSelection"
      ]
    },
    {
      "page": "filterVariants",
      "title": "Function: filterVariants ----------- This function takes a SingleCellExperiment object as input and performs variant filtering",
      "topics": [
        "filterVariants"
      ]
    },
    {
      "page": "h5ToSce",
      "title": "Function: h5ToSce This function takes the path of an h5 file and reads this into an object of the SingleCellExperiment class.",
      "topics": [
        "h5ToSce"
      ]
    },
    {
      "page": "launchScafariShiny",
      "title": "Launch Scafari Shiny Application",
      "topics": [
        "launchScafariShiny"
      ]
    },
    {
      "page": "logLogPlot",
      "title": "Plot a log-log plot for read counts",
      "topics": [
        "logLogPlot"
      ]
    },
    {
      "page": "normalizeReadCounts",
      "title": "This function normalizes the read counts contained within a `SingleCellExperiment` object.",
      "topics": [
        "normalizeReadCounts"
      ]
    },
    {
      "page": "plotAmpliconDistribution",
      "title": "Plot Distribution of Amplicons",
      "topics": [
        "plotAmpliconDistribution"
      ]
    },
    {
      "page": "plotClusterGenotype",
      "title": "Plot Genotype Clusters",
      "topics": [
        "plotClusterGenotype"
      ]
    },
    {
      "page": "plotClusterVAF",
      "title": "plot Cluster VAF This function generates a plot to visualize variant allele frequency (VAF) in clusters based on selected variants of interest.",
      "topics": [
        "plotClusterVAF"
      ]
    },
    {
      "page": "plotClusterVAFMap",
      "title": "plot Cluster VAF Map This function generates a plot to visualize variant allele frequency (VAF) in clusters based on selected variants of interest with clusters in the background.",
      "topics": [
        "plotClusterVAFMap"
      ]
    },
    {
      "page": "plotElbow",
      "title": "This function takes a SingleCellExperiment object and variants of interest as input and plots an elbow plot to perform k-means later.",
      "topics": [
        "plotElbow"
      ]
    },
    {
      "page": "plotGenotypequalityPerGenotype",
      "title": "Plot Genotype Quality per Genotype",
      "topics": [
        "plotGenotypequalityPerGenotype"
      ]
    },
    {
      "page": "plotNormalizedReadCounts",
      "title": "Plot normalized read counts",
      "topics": [
        "plotNormalizedReadCounts"
      ]
    },
    {
      "page": "plotPanelUniformity",
      "title": "Plot Panel Uniformity",
      "topics": [
        "plotPanelUniformity"
      ]
    },
    {
      "page": "plotVariantHeatmap",
      "title": "Plot Variant Heatmap",
      "topics": [
        "plotVariantHeatmap"
      ]
    },
    {
      "page": "scafari",
      "title": "scafari: analyzing scDNA-seq data",
      "topics": [
        "scafari-package",
        "scafari"
      ]
    }
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