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  "Title": "Automated PhIP-seq Analysis and Reporting",
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  "Description": "Provides an end-to-end toolkit for Phage\nImmunoPrecipitation- sequencing (PhIP-seq) data. Functions\nimport raw peptide-sample count matrices, apply quality control\nfilters, normalise library sizes, compute enrichment statistics\nand diversity metrics, and identify differentially enriched\npeptides or motifs. Results can be explored through tidy data\nframes, visualised with publication-ready ggplot2 graphics, or\nrendered into fully fledged HTML reports via R Markdown.",
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  "Repository": "https://polymerase3.r-universe.dev",
  "Date/Publication": "2026-04-15 18:35:49 UTC",
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  "Author": "Mateusz Kolek [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0001-6470-4830>),\nAlon Alexander [ctb, cph],\nThomas Vogl [cph, fnd] (ORCID: <https://orcid.org/0000-0002-3892-1740>)",
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      "title": "Test Homogeneity of Dispersion (Beta Dispersion)",
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    {
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      "title": "PERMANOVA with Global and Post-hoc Tests on Beta Diversity",
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      "title": "Prevalence comparison by group (POP framework)",
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    },
    {
      "page": "compute_tsne",
      "title": "Compute t-SNE Embeddings for Sample Distances",
      "topics": [
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    {
      "page": "deltaplot",
      "title": "Delta-prevalence vs Pooled Prevalence",
      "topics": [
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    {
      "page": "deltaplot_interactive",
      "title": "Interactive Delta-prevalence vs Pooled Prevalence",
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      "page": "ecdf_plot",
      "title": "ECDF of Per-peptide Prevalences for Two Groups",
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    {
      "page": "ecdf_plot_interactive",
      "title": "ECDF of Per-peptide Prevalence for Two Groups",
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      "title": "PHIP default colour palette",
      "topics": [
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        "What's in the output?",
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        "Multiple ranks",
        "Group interactions",
        "Selecting a metric subset",
        "Shannon base",
        "Presence modes",
        "mode = \"binary\" (default)",
        "mode = \"threshold\"",
        "mode = \"abundance\"",
        "Accessing result attributes",
        "Visualising alpha diversity",
        "plot_alpha() — static boxplots",
        "All five metrics",
        "Faceting across multiple ranks",
        "Filtering and ordering groups",
        "Customising appearance",
        "Plotting the interaction table",
        "plot_alpha_interactive() — plotly",
        "Statistical testing",
        "Default: Kruskal-Wallis + Wilcoxon",
        "Global test",
        "Pairwise comparisons",
        "Choosing the test",
        "p-value adjustment",
        "Restricting to a subset of metrics",
        "Multi-rank significance",
        "Visualising significance",
        "Table mode",
        "Heatmap mode",
        "Heatmap across metrics",
        "Significance brackets on boxplots",
        "Putting it all together",
        "Session info"
      ],
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      "modified": "2026-03-28 14:56:35",
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    {
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      "filename": "beta-diversity.html",
      "title": "Beta Diversity Analysis in PhIP-seq",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Setup",
        "Step 1 — Distance matrix",
        "Choosing a distance and normalisation",
        "Step 2 — Unconstrained ordination (PCoA)",
        "Computing PCoA",
        "Scree plot",
        "Feature associations",
        "Plotting PCoA",
        "Basic plot — colour by group",
        "Adding a time factor",
        "Centroids and centroid trajectories",
        "Confidence ellipses",
        "Plotting alternative axes",
        "Step 3 — Constrained ordination (CAP / db-RDA)",
        "Plotting CAP",
        "Step 4 — PERMANOVA",
        "Step 5 — Beta dispersion",
        "Plotting dispersion",
        "Group dispersion",
        "Time dispersion",
        "Step 6 — t-SNE",
        "2D plot",
        "3D interactive plot",
        "Putting it all together",
        "Session info"
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      "filename": "delta-analysis.html",
      "title": "Delta Analysis in PhIP-seq",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Setup",
        "Visualising prevalence shift",
        "deltaplot() — static ggplot2",
        "Adjusting the smooth",
        "Jitter and appearance",
        "deltaplot_interactive() — plotly",
        "Testing global shift: compute_delta()",
        "Unpaired design — group comparison",
        "What's in the output?",
        "Choosing the per-peptide statistic",
        "Aggregation and stratification",
        "Weighting",
        "Paired design — timepoint comparison",
        "Forest plots",
        "forestplot() — static ggplot2",
        "Diverging colours",
        "Filtering to significant features",
        "forestplot_interactive() — plotly",
        "Putting it all together",
        "Session info"
      ],
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      "modified": "2026-04-15 18:35:49",
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    {
      "source": "pop-analysis.Rmd",
      "filename": "pop-analysis.html",
      "title": "Prevalence of Presence (POP) Analysis in PhIP-seq",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Setup",
        "Computing prevalence: compute_pop()",
        "Unpaired design — group comparison",
        "What's in the output?",
        "Multiple group columns",
        "Multiple ranks",
        "k-of-n presence threshold",
        "Paired design — timepoint comparison",
        "Scatter plots",
        "scatter_static() — ggplot2",
        "scatter_interactive() — plotly",
        "Volcano plots",
        "volcano_static() — ggplot2",
        "Cutoffs",
        "BH correction",
        "volcano_interactive() — plotly",
        "Putting it all together",
        "Session info"
      ],
      "created": "2026-04-15 18:35:49",
      "modified": "2026-04-15 18:35:49",
      "commits": 1
    }
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