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Single-cell study — samples before cell counts

Design a single-cell analysis without treating cells from one donor as independent biological replicates. Track sample identity through quality control, annotation and donor-level comparisons.

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{
  "nodes": [
    { "id": "don", "type": "rounded", "label": "Independent donor samples", "x": 40, "y": 200, "width": 150, "height": 104, "fill": "#ede9fe", "stroke": "#6d28d9" },
    { "id": "meta", "type": "card", "label": "Donor / batch metadata", "x": 40, "y": 520, "width": 150, "height": 104, "fill": "#ccfbf1", "stroke": "#0f766e" },
    { "id": "lib", "type": "rounded", "label": "Library preparation", "x": 215, "y": 200, "width": 150, "height": 104, "fill": "#fef3c7", "stroke": "#b45309" },
    { "id": "qc", "type": "octagon", "label": "Cell and gene quality checks", "x": 390, "y": 200, "width": 150, "height": 104, "fill": "#e0f2fe", "stroke": "#0369a1" },
    { "id": "dbl", "type": "octagon", "label": "Doublet / ambient RNA review", "x": 390, "y": 520, "width": 150, "height": 104, "fill": "#e0f2fe", "stroke": "#0369a1" },
    { "id": "norm", "type": "rounded", "label": "Normalise and explore", "x": 565, "y": 200, "width": 150, "height": 104, "fill": "#fef3c7", "stroke": "#b45309" },
    { "id": "ann", "type": "rounded", "label": "Annotate with marker evidence", "x": 740, "y": 200, "width": 150, "height": 104, "fill": "#fef3c7", "stroke": "#b45309" },
    { "id": "agg", "type": "rounded", "label": "Aggregate within donor and type", "x": 740, "y": 520, "width": 150, "height": 104, "fill": "#fef3c7", "stroke": "#b45309" },
    { "id": "cmp", "type": "card", "label": "Compare donor-level responses", "x": 915, "y": 520, "width": 150, "height": 104, "fill": "#ccfbf1", "stroke": "#0f766e" },
    { "id": "sens", "type": "rounded", "label": "Sensitivity across QC choices", "x": 915, "y": 200, "width": 150, "height": 104, "fill": "#f1f5f9", "stroke": "#475569" }
  ],
  "edges": [
    { "id": "e0", "source": "don", "target": "lib", "label": "prepare" },
    { "id": "e1", "source": "lib", "target": "qc", "label": "reads" },
    { "id": "e2", "source": "qc", "target": "norm", "label": "retained cells" },
    { "id": "e3", "source": "dbl", "target": "norm", "label": "exclude artifacts", "style": "dashed" },
    { "id": "e4", "source": "meta", "target": "agg", "label": "preserve sample identity", "style": "dashed" },
    { "id": "e5", "source": "norm", "target": "ann", "label": "clusters" },
    { "id": "e6", "source": "ann", "target": "agg", "label": "cell types" },
    { "id": "e7", "source": "agg", "target": "cmp", "label": "biological replicates" },
    { "id": "e8", "source": "ann", "target": "sens", "label": "annotation uncertainty" },
    { "id": "e9", "source": "cmp", "target": "sens", "label": "robustness" }
  ]
}