dmsa/_pkgdown.yml at main · teindor/dmsa · GitHub

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url: https://teindor.github.io/dmsa

template:
  bootstrap: 5
  includes:
    in_header: |
      <script type="application/ld+json">
      {
        "@context": "https://schema.org",
        "@type": "SoftwareSourceCode",
        "name": "dmsa",
        "alternateName": "Directional Methylation Set Analysis",
        "description": "Directional Methylation Set Analysis (DMSA) is an R package for gene-set and system-level analysis of DNA methylation array data. Before aggregating, DMSA aligns each probe's effect to that probe's predicted consequence for gene expression, so probes predicted to raise expression and probes predicted to lower it are no longer averaged against each other. Each unit's statistic is computed from that unit's own probes alone, and multiplicity is corrected only within level-local families. In a benchmark where opposing effects cancelled under conventional aggregation, DMSA reached 84% power against 7-8% for camera, fry and over-representation alternatives, and reported the correct biological direction in 100% of its detections. Where the question was instead whether a whole panel was associated, DMSA's pooled score stayed silent while globaltest correctly rejected.",
        "codeRepository": "https://github.com/teindor/dmsa",
        "programmingLanguage": { "@type": "ComputerLanguage", "name": "R" },
        "license": "https://spdx.org/licenses/MIT.html",
        "identifier": "https://doi.org/10.5281/zenodo.22023957",
        "applicationCategory": "Bioinformatics",
        "keywords": ["DNA methylation","gene set analysis","epigenetics",
                     "EWAS","directional inference","permutation testing"],
        "author": {
          "@type": "Person",
          "name": "Tsachi Ein-Dor",
          "identifier": "https://orcid.org/0000-0002-3078-7591",
          "affiliation": {
            "@type": "Organization",
            "name": "Reichman University"
          }
        }
      }
      </script>

home:
  title: dmsa - Directional Methylation Set Analysis
  description: >
    Aligns probe-level DNA methylation effects to their predicted consequence
    for gene expression before aggregating, tests each unit through three
    pre-specified lenses on one permutation stream, and names the responsible
    gene inside level-local families with family-wise error control.

navbar:
  structure:
    left: [intro, reference, articles, news]
    right: [search, github]

reference:
  - title: The two-call interface
    desc: Declare the design once, run it once.
    contents: [dmsa_frame, dmsa_report, dmsa_report_panels]
  - title: Bioconductor interoperability
    desc: Working from a SummarizedExperiment.
    contents: [dmsa_se]
  - title: Alignment and testing
    desc: The directional chain and the three lenses.
    contents: [dmsa_align, dmsa_directions, dmsa_triangulate,
               dmsa_test, dmsa_pdance,
               dmsa_score, dmsa_scores,
               dmsa_relweights, dmsa_perm_pvalue, dmsa_omnibus]
  - title: Selection and hierarchy
    contents: [dmsa_sets, dmsa_select, dmsa_cascade, dmsa_systems, dmsa_levels,
               dmsa_tree, dmsa_sets_check, dmsa_sets_template, dmsa_cascade_null]
  - title: Polarity and reference maps
    contents: [dmsa_polarity, dmsa_polarity_check, dmsa_polarity_for,
               dmsa_polarity_fetch, dmsa_polarity_review, dmsa_polarity_sources,
               dmsa_reference, dmsa_reference_csv, dmsa_reference_read,
               dmsa_reference_template, dmsa_reference_write, dmsa_evidence,
               alpha_polarity, alpha_gene_systems, alpha_reference, alpha_design]
  - title: Design, models and extensions
    contents: [dmsa_design, dmsa_check_design, dmsa_model, dmsa_model_omnibus,
               dmsa_fit, dmsa_moderate, dmsa_change, dmsa_outcome, dmsa_contrasts,
               dmsa_contrast_adjust, dmsa_mvalues, dmsa_gate, dmsa_balance]
  - title: Multiplicity
    contents: [dmsa_lfdr, dmsa_bfdr_select]
  - title: Figures
    contents: [dmsa_plot_genes, dmsa_plot_locus, dmsa_plot_locus_gviz,
               dmsa_plot_probes, dmsa_plot_systems, dmsa_gene_model,
               dmsa_gene_model_check]
  - title: Coordinates and annotation
    contents: [dmsa_probe_coords, dmsa_probe_annotation_template,
               dmsa_write_coords, dmsa_test_drive]