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  "Package": "fastCNV",
  "Title": "Fast CNV Detection for Single-Cell and Spatial Transcriptomics",
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  "Description": "Fast and accurate detection of Copy Number Variations\n(CNVs) in single-cell RNA sequencing (scRNA-seq) and Spatial\nTranscriptomics (ST) data, including 10X Visium and Visium HD.\nProvides sliding window-based CNV inference, hierarchical\nclustering of CNV profiles, and publication-ready\nvisualization. Compatible with Seurat 4.x/5.x.",
  "License": "GPL-3",
  "URL": "https://zaoqu-liu.github.io/fastCNV/,\nhttps://github.com/Zaoqu-Liu/fastCNV",
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  "Repository": "https://zaoqu-liu.r-universe.dev",
  "Date/Publication": "2026-01-23 12:41:17 UTC",
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  "Author": "Zaoqu Liu [cre, aut],\nGadea Cabrejas [aut, cph],\nClarice Groeneveld [aut]",
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      "page": "annotateCNVTree",
      "title": "Annotate a Phylogenetic Tree with CNV Events",
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    },
    {
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      "title": "Project 8µm Spatial Annotation onto 16µm Spots",
      "topics": [
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      "page": "buildCNVTree",
      "title": "Construct a Phylogenetic Tree from a Copy Number Variation (CNV) Matrix",
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    },
    {
      "page": "CNVAnalysis",
      "title": "CNVAnalysis Runs Copy Number Variation (CNV) analysis on a Seurat object or a list of Seurat objects.",
      "topics": [
        "CNVAnalysis"
      ]
    },
    {
      "page": "CNVCalling",
      "title": "CNVCalling Performs Copy Number Variation (CNV) analysis on a Seurat object.",
      "topics": [
        "CNVCalling"
      ]
    },
    {
      "page": "CNVCallingList",
      "title": "CNVCalling for a List of Seurat Objects Performs Copy Number Variation (CNV) analysis on a list of Seurat objects.",
      "topics": [
        "CNVCallingList"
      ]
    },
    {
      "page": "CNVClassification",
      "title": "CNV Classification Classifies the CNV results into loss, gain, or no alteration for each observation and chromosome arm.",
      "topics": [
        "CNVClassification"
      ]
    },
    {
      "page": "CNVCluster",
      "title": "Perform CNV Clustering with Seurat Object",
      "topics": [
        "CNVCluster"
      ]
    },
    {
      "page": "CNVPerChromosomeArm",
      "title": "CNV Per Chromosome Arm Computes the CNV fraction of each spot/cell per chromosome arm, then stores the results into the metadata.",
      "topics": [
        "CNVPerChromosomeArm"
      ]
    },
    {
      "page": "CNVTree",
      "title": "Build, annotate and plot a Phylogenetic Tree from a seurat Object containing the CNV results from 'fastCNV()'",
      "topics": [
        "CNVTree"
      ]
    },
    {
      "page": "computeAverageExpression",
      "title": "Compute average expression for patients",
      "topics": [
        "computeAverageExpression"
      ]
    },
    {
      "page": "fastCNV",
      "title": "Fast CNV Detection for Single-Cell and Spatial Transcriptomics Data",
      "topics": [
        "fastCNV"
      ]
    },
    {
      "page": "fastCNV_10XHD",
      "title": "fastCNV_10XHD calls all of the internal functions needed to compute the putative CNV on a Seurat Visium HD object or a list of Seurat Visium HD objects",
      "topics": [
        "fastCNV_10XHD"
      ]
    },
    {
      "page": "geneMetadata",
      "title": "Genes Data from Ensembl Version 113",
      "topics": [
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    },
    {
      "page": "generateCNVClonesMatrix",
      "title": "Generate CNV Matrix for CNV Clusters by Chromosome Arm",
      "topics": [
        "generateCNVClonesMatrix"
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    },
    {
      "page": "getGenes",
      "title": "Download Gene Information from Ensembl",
      "topics": [
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    },
    {
      "page": "mergeCNVClusters",
      "title": "Merge CNV Clusters in a Seurat Object",
      "topics": [
        "mergeCNVClusters"
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    },
    {
      "page": "plotCNVResults",
      "title": "Plot CNV Results into a Heatmap Builds a heatmap to visualize the CNV results based on genomic scores.",
      "topics": [
        "plotCNVResults"
      ]
    },
    {
      "page": "plotCNVResultsHD",
      "title": "Plot Visium HD CNV Results into a Heatmap Builds a heatmap to visualize the Visium HD CNV results based on genomic scores.",
      "topics": [
        "plotCNVResultsHD"
      ]
    },
    {
      "page": "plotCNVTree",
      "title": "Plot an Annotated Phylogenetic Tree with CNV Events",
      "topics": [
        "plotCNVTree"
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    },
    {
      "page": "prepareCountsForCNVAnalysis",
      "title": "Aggregate Observations by Cell Type for CNV Analysis Aggregates observations with the same cell types to increase counts per observation, improving Copy Number Variation (CNV) computation.",
      "topics": [
        "prepareCountsForCNVAnalysis"
      ]
    }
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      "title": "Advanced Visualization",
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      "headings": [
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        "Expression-Based CNV Inference",
        "Algorithm Pipeline",
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        "Step 2: Sliding Window Smoothing",
        "Step 3: Reference Normalization",
        "Step 4: Score Computation",
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    {
      "source": "introduction.Rmd",
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      "title": "Introduction to fastCNV",
      "author": "Zaoqu Liu",
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      "headings": [
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        "Installation",
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        "Quick Start",
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        "Understanding the Parameters",
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    {
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      "filename": "multi-sample.html",
      "title": "Multi-Sample Analysis",
      "author": "Zaoqu Liu",
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      "headings": [
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        "Loading Samples",
        "Sample List Preparation",
        "Running Multi-Sample Analysis",
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        "Pooled Reference Analysis",
        "Handling Results",
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