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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": "2026-10-08 08:40:42 UTC",
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  "Author": "Mateusz Kolek [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0001-6470-4830>),\nAlon Alexander [cph] (contributed code and shaped the package concept),\nNikolas Basler [ctb] (ORCID: <https://orcid.org/0000-0003-0791-4369>),\nThomas Vogl [cph, fnd] (ORCID: <https://orcid.org/0000-0002-3892-1740>)",
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      "title": "Compute alpha diversity per sample / group across ranks",
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      "topics": [
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    {
      "page": "compute_dispersion",
      "title": "Test Homogeneity of Dispersion (Beta Dispersion)",
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    {
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      "title": "Compute Pairwise Sample Distances",
      "topics": [
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    {
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      "title": "Principal Components Analysis (PCoA) on a Distance Matrix",
      "topics": [
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    },
    {
      "page": "compute_pcoa_feature_associations",
      "title": "Compute Feature Associations to PCoA Vectors",
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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)",
      "topics": [
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    {
      "page": "compute_tsne",
      "title": "Compute t-SNE Embeddings for Sample Distances",
      "topics": [
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    {
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      "title": "Delta-prevalence vs Pooled Prevalence",
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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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      "page": "forestplot",
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    {
      "page": "forestplot_interactive",
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      "title": "PHIP default colour palette",
      "topics": [
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      "title": "Plot alpha diversity (richness/Shannon/Simpson) from precomputed results",
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      "title": "Visualise alpha diversity significance results",
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      "title": "Static volcano plot (log2 ratio vs -log10 p)",
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