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  "Package": "SCpubr",
  "Title": "Generate Publication Ready Visualizations of Single Cell\nTranscriptomics Data",
  "Version": "3.0.1",
  "Authors@R": "person(\"Enrique\", \"Blanco-Carmona\", , \"scpubr@gmail.com\", role = c(\"cre\", \"aut\"),\ncomment = c(ORCID = \"0000-0002-1208-1691\"))",
  "Description": "A system that provides a streamlined way of generating\npublication ready plots for known Single-Cell transcriptomics\ndata in a “publication ready” format. This is, the goal is to\nautomatically generate plots with the highest quality possible,\nthat can be used right away or with minimal modifications for a\nresearch article.",
  "License": "GPL-3",
  "URL": "https://github.com/enblacar/SCpubr/,\nhttps://enblacar.github.io/SCpubr-book/",
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  "Repository": "https://enblacar.r-universe.dev",
  "Date/Publication": "2026-03-02 09:25:10 UTC",
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  "Author": "Enrique Blanco-Carmona [cre, aut] (ORCID:\n<https://orcid.org/0000-0002-1208-1691>)",
  "Maintainer": "Enrique Blanco-Carmona <scpubr@gmail.com>",
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    "do_ChordDiagramPlot",
    "do_CNVHeatmap",
    "do_ColorBlindCheck",
    "do_ColorPalette",
    "do_CorrelationHeatmap",
    "do_DimPlot",
    "do_DotPlot",
    "do_EnrichmentHeatmap",
    "do_ExpressionHeatmap",
    "do_FeaturePlot",
    "do_GroupwiseDEHeatmap",
    "do_LigandReceptorPlot",
    "do_LoadingsHeatmap",
    "do_MetadataHeatmap",
    "do_NebulosaPlot",
    "do_PackageReport",
    "do_PathwayActivityHeatmap",
    "do_RankedEnrichmentHeatmap",
    "do_RankedExpressionHeatmap",
    "do_RidgePlot",
    "do_SCEnrichmentHeatmap",
    "do_SCExpressionHeatmap",
    "do_StripPlot",
    "do_TermEnrichmentPlot",
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    "do_ViolinPlot",
    "do_VolcanoPlot",
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        "tbl",
        "data.frame"
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        "arm",
        "start",
        "end"
      ],
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      "table": true,
      "tojson": true
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      "page": "do_ActivityHeatmap",
      "title": "Compute affinity of gene sets to cell populations using decoupleR.",
      "topics": [
        "do_ActivityHeatmap"
      ]
    },
    {
      "page": "do_AlluvialPlot",
      "title": "Generate Alluvial plots.",
      "topics": [
        "do_AlluvialPlot"
      ]
    },
    {
      "page": "do_BarPlot",
      "title": "Create Bar Plots.",
      "topics": [
        "do_BarPlot"
      ]
    },
    {
      "page": "do_BeeSwarmPlot",
      "title": "Generate BeeSwarm plots of ranked cells colored by gene expression or metadata.",
      "topics": [
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      ]
    },
    {
      "page": "do_BoxPlot",
      "title": "Generate Box Plots.",
      "topics": [
        "do_BoxPlot"
      ]
    },
    {
      "page": "do_CellularStatesPlot",
      "title": "Plot relationships between enrichment scores to infer cellular states.",
      "topics": [
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      ]
    },
    {
      "page": "do_ChordDiagramPlot",
      "title": "Generate a Chord diagram.",
      "topics": [
        "do_ChordDiagramPlot"
      ]
    },
    {
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      "title": "Display CNV scores from inferCNV as Feature Plots.",
      "topics": [
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    },
    {
      "page": "do_ColorBlindCheck",
      "title": "Generate colorblind variations of a given color palette.",
      "topics": [
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    },
    {
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      "title": "Generate color scales based on a value.",
      "topics": [
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    },
    {
      "page": "do_CorrelationHeatmap",
      "title": "Create correlation matrix heatmaps.",
      "topics": [
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      ]
    },
    {
      "page": "do_DimPlot",
      "title": "Generate dimensional reduction plots from a Seurat object.",
      "topics": [
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      ]
    },
    {
      "page": "do_DotPlot",
      "title": "Generate Dot plots of gene expression across cell groups.",
      "topics": [
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      ]
    },
    {
      "page": "do_EnrichmentHeatmap",
      "title": "Create enrichment scores heatmaps.",
      "topics": [
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      ]
    },
    {
      "page": "do_ExpressionHeatmap",
      "title": "Create heatmaps of averaged expression by groups.",
      "topics": [
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      ]
    },
    {
      "page": "do_FeaturePlot",
      "title": "Plot gene expression on dimensional reduction embeddings.",
      "topics": [
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      ]
    },
    {
      "page": "do_GroupwiseDEHeatmap",
      "title": "Compute a dotplot with the results of a group-wise DE analysis.",
      "topics": [
        "do_GroupwiseDEHeatmap"
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    },
    {
      "page": "do_LigandReceptorPlot",
      "title": "Visualize Ligand-Receptor analysis output.",
      "topics": [
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    },
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      "page": "do_LoadingsHeatmap",
      "title": "Compute a heatmap summary of the top and bottom genes in the PCA loadings for the desired PCs in a Seurat object.",
      "topics": [
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      ]
    },
    {
      "page": "do_MetadataHeatmap",
      "title": "Compute a heatmap of categorical variables.",
      "topics": [
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      ]
    },
    {
      "page": "do_NebulosaPlot",
      "title": "Plot kernel density estimates of gene expression on dimensional reduction embeddings.",
      "topics": [
        "do_NebulosaPlot"
      ]
    },
    {
      "page": "do_PackageReport",
      "title": "Generate a status report of SCpubr and its dependencies.",
      "topics": [
        "do_PackageReport"
      ]
    },
    {
      "page": "do_PathwayActivityHeatmap",
      "title": "Plot Pathway Activities from decoupleR using Progeny prior knowledge.",
      "topics": [
        "do_PathwayActivityHeatmap"
      ]
    },
    {
      "page": "do_RankedEnrichmentHeatmap",
      "title": "Compute a heatmap of enrichment of gene sets on the context of a dimensional reduction component.",
      "topics": [
        "do_RankedEnrichmentHeatmap"
      ]
    },
    {
      "page": "do_RankedExpressionHeatmap",
      "title": "Compute a heatmap of expression of genes on the context of a dimensional reduction component.",
      "topics": [
        "do_RankedExpressionHeatmap"
      ]
    },
    {
      "page": "do_RidgePlot",
      "title": "Create ridge plots.",
      "topics": [
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      ]
    },
    {
      "page": "do_SCEnrichmentHeatmap",
      "title": "Perform a single-cell-based heatmap showing the enrichment in a list of gene sets.",
      "topics": [
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      ]
    },
    {
      "page": "do_SCExpressionHeatmap",
      "title": "Perform a single-cell-based heatmap showing the expression of genes.",
      "topics": [
        "do_SCExpressionHeatmap"
      ]
    },
    {
      "page": "do_StripPlot",
      "title": "Generate a Strip plot.",
      "topics": [
        "do_StripPlot"
      ]
    },
    {
      "page": "do_TermEnrichmentPlot",
      "title": "Display the enriched terms for a given list of genes.",
      "topics": [
        "do_TermEnrichmentPlot"
      ]
    },
    {
      "page": "do_TFActivityHeatmap",
      "title": "Plot TF Activities from decoupleR using Dorothea prior knowledge.",
      "topics": [
        "do_TFActivityHeatmap"
      ]
    },
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      "page": "do_ViolinPlot",
      "title": "Generate Violin plots from a Seurat object.",
      "topics": [
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      ]
    },
    {
      "page": "do_VolcanoPlot",
      "title": "Compute a Volcano plot out of DE genes.",
      "topics": [
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      ]
    },
    {
      "page": "do_WafflePlot",
      "title": "Generate Waffle plots to display cell group proportions.",
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        "do_WafflePlot"
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    },
    {
      "page": "human_chr_locations",
      "title": "Chromosome arm locations for human genome GRCh38.",
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