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  "Title": "Predict cis-co-accessibility from single-cell chromatin\naccessibility data",
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  "Description": "Cicero computes putative cis-regulatory maps from\nsingle-cell chromatin accessibility data. It also extends\nmonocle 2 for use in chromatin accessibility data.",
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      "title": "Single Cell ATAC-seq Analysis with Cicero",
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      "headings": [
        "Introduction:",
        "Installing Cicero",
        "Constructing cis-regulatory networks",
        "Running Cicero",
        "The CellDataSet class",
        "Create a Cicero CDS",
        "Run Cicero",
        "Visualizing Cicero Connections",
        "Comparing Cicero connections to other datasets",
        "Finding Cis-Coaccessibility Networks (CCANS)",
        "Cicero gene activity scores",
        "Single-cell accessibility trajectories",
        "Constructing trajectories with accessibility data",
        "Aggregation: the primary method for addressing sparsity",
        "aggregate_nearby_peaks",
        "Choose sites for dimensionality reduction",
        "Choosing sites that define progress",
        "Choose sites by differential analysis",
        "Choose sites by dpFeature",
        "Reduce the dimensionality of the data and order cells",
        "Differential Accessibility Analysis",
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        "Running differentialGeneTest with single-cell chromatin accessibility data",
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        "References",
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      "created": "2018-05-09 18:08:03",
      "modified": "2026-03-18 17:06:40",
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