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  "Title": "Longitudinal Integration Site Analysis Toolkit",
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  "Authors@R": "person(\"Shuai\", \"Ni\", , \"Nishuai@wakerbio.com\", role = c(\"aut\", \"cre\"))",
  "Description": "A comprehensive toolkit for the analysis of longitudinal\nintegration site data, including data cleaning, quality\ncontrol, statistical modeling, and visualization. It\nstreamlines the entire workflow of integration site analysis,\nsupports simple input formats, and provides user-friendly\nfunctions for researchers in virus integration site analysis.\nNi et al. (2025) <doi:10.64898/2025.12.20.695672>.",
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    "CIS_overlap",
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      "page": "chr_distribution",
      "title": "Plot chromosome distribution of integration sites (IS)",
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        "chr_distribution"
      ]
    },
    {
      "page": "CIS",
      "title": "Visualize and analyze network of common integration sites (CIS)",
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        "CIS"
      ]
    },
    {
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      "title": "Generate colored GT table for CIS overlap across samples/timepoints",
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        "CIS_overlap"
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    },
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      "title": "Calculate regional distribution percentages of integration sites (IS)",
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        "Count_regions"
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    },
    {
      "page": "Enhancer_check",
      "title": "Check if integration sites (IS) are located in enhancer regions",
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        "Enhancer_check"
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    },
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      "title": "Calculate normalized cumulative sum for top N elements of a numeric vector",
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    },
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      "page": "get_feature",
      "title": "Annotate integration site (IS) data with genomic features",
      "topics": [
        "get_feature"
      ]
    },
    {
      "page": "ideogram_plot",
      "title": "Plot chromosome ideogram with integration site annotations",
      "topics": [
        "ideogram_plot"
      ]
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    {
      "page": "is_in_AE_gene",
      "title": "Plot AE-associated gene clone contribution",
      "topics": [
        "is_in_AE_gene"
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    },
    {
      "page": "is_in_CG_gene",
      "title": "Plot Cancer-associated gene clone contribution",
      "topics": [
        "is_in_CG_gene"
      ]
    },
    {
      "page": "is_in_immune_gene",
      "title": "Plot Immune-associated gene clone contribution",
      "topics": [
        "is_in_immune_gene"
      ]
    },
    {
      "page": "IS_treemap",
      "title": "Generate treemap of integration site clone contribution",
      "topics": [
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    },
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      "title": "Generate Linked Timepoint Sankey + Stacked Bar Chart",
      "topics": [
        "Linked_timepoints"
      ]
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      "title": "Plot Region-wise Donut Charts",
      "topics": [
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    },
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      "page": "pmd_analysis",
      "title": "Calculate PMD (Proportional Modular Diversity) for integration site data",
      "topics": [
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    },
    {
      "page": "pmd_plot",
      "title": "Generate PMD (Proportional Modular Diversity) Scatter Plot with Inset Legend",
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        "pmd_plot"
      ]
    },
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      "title": "Check if integration sites (IS) are located in promoter regions",
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      "title": "Check if integration sites (IS) are located in safe harbor regions",
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      "title": "Validate and standardize integration site (IS) raw data frame",
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