echoAI/_pkgdown.yml at main · RajLabMSSM/echoAI · GitHub

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url: https://rajlabmssm.github.io/echoAI/

template:
  bootstrap: 5
  bslib:
    bg: "#1a2744"
    fg: "#e8f4f4"
    primary: "#4ecdc4"
    secondary: "#3a8d8c"
    success: "#2ee8d6"
    info: "#5bc0be"
    code-bg: "#d6e4ee"
    code-color: "#1a2744"
    border-color: "#2a4060"
    link-color: "#4ecdc4"
    link-hover-color: "#2ee8d6"
    font-size-base: "1rem"
  includes:
    in_header: |
      <style>
      .navbar {
        background-color: #162038 !important;
        border-bottom: 2px solid #4ecdc4;
      }
      .navbar-brand, .nav-link { color: #e8f4f4 !important; }
      .nav-link:hover { color: #2ee8d6 !important; }
      .nav-link.active { color: #2ee8d6 !important; border-bottom: 2px solid #2ee8d6; }
      pre {
        background-color: #d6e4ee !important;
        color: #1a2744 !important;
        border: none !important;
        border-radius: 12px;
        margin: 0;
        padding: 0.8em 1em;
      }
      code { color: #1a6b68 !important; border: none !important; }
      pre code { color: #1a2744 !important; border: none !important; background: transparent !important; }
      pre code span { border: none !important; background: transparent !important; }
      .table { color: #e8f4f4 !important; }
      .table-striped > tbody > tr:nth-of-type(odd) > * {
        background-color: rgba(78, 205, 196, 0.05) !important;
        color: #e8f4f4 !important;
      }
      .table-striped > tbody > tr:nth-of-type(even) > * {
        background-color: transparent !important;
        color: #e8f4f4 !important;
      }
      .table > thead { border-bottom: 2px solid #4ecdc4; }
      h1, h2, h3, h4, h5, h6 { color: #4ecdc4 !important; }
      a { color: #5bc0be; }
      a:hover { color: #2ee8d6; }
      .card { background-color: #1e3050; border-color: #2a4060; }
      .footer { background-color: #162038 !important; border-top: 1px solid #2a4060; }
      .page-header { border-bottom: 2px solid #3a8d8c; }
      .sourceCode {
        background-color: #d6e4ee !important;
        border: 1px solid #3a8d8c;
        border-radius: 12px !important;
        overflow: hidden;
      }
      .sourceCode code span,
      .sourceCode code a {
        border: none !important;
        outline: none !important;
        box-shadow: none !important;
        background: transparent !important;
      }
      </style>

navbar:
  structure:
    left: [intro, reference, articles, news]
    right: [search, github]
  components:
    github:
      icon: fa-github
      href: https://github.com/RajLabMSSM/echoAI

articles:
  - title: Getting started
    contents:
      - echoAI
  - title: Setup
    contents:
      - docker

reference:
  - title: IMPACT annotations
    desc: Query and process IMPACT transcription factor binding predictions
    contents:
      - IMPACT_query
      - IMPACT_get_annotations
      - IMPACT_iterate_get_annotations
      - IMPACT_get_annotation_key
      - IMPACT_get_ldscores
      - IMPACT_get_top_annotations
      - IMPACT_postprocess_annotations
  - title: IMPACT enrichment
    desc: Compute and visualise enrichment of IMPACT scores across SNP groups
    contents:
      - IMPACT_compute_enrichment
      - IMPACT_iterate_enrichment
  - title: IMPACT visualisation
    desc: Plots for IMPACT scores and enrichment results
    contents:
      - IMPACT_plot_enrichment
      - IMPACT_plot_impact_score
      - IMPACT_snp_group_boxplot
      - IMPACT_heatmap
  - title: SpliceAI
    desc: Query and visualise SpliceAI splice-site predictions
    contents:
      - SPLICEAI_run
      - SPLICEAI_query_api
      - SPLICEAI_query_tsv
      - SPLICEAI_query_tsv_iterate
      - SPLICEAI_query_vcf
      - SPLICEAI_snp_probs
      - SPLICEAI_plot
  - title: Deep learning annotations
    desc: Query and visualise Basenji/DeepSEA predictions
    contents:
      - DEEPLEARNING_query
      - DEEPLEARNING_query_multi_chr
      - DEEPLEARNING_query_one_chr
      - DEEPLEARNING_melt
      - DEEPLEARNING_plot

  - title: Bundled data
    contents:
      - IMPACT_files