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

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

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

articles:
  - title: Getting Started
    contents:
      - echoLD

reference:
  - title: LD Retrieval
    desc: Retrieve LD matrices from reference panels or custom sources.
    contents:
      - get_LD
      - get_LD_matrix
      - get_LD_vcf

  - title: LD Blocks
    desc: Identify and work with LD blocks.
    contents:
      - get_LD_blocks
      - get_lead_r2

  - title: LD Filtering and Conversion
    desc: Filter, convert, and transform LD matrices.
    contents:
      - filter_LD
      - r2_to_r
      - subset_common_snps

  - title: Sparse Matrix I/O
    desc: Read, write, and convert sparse LD matrices.
    contents:
      - readSparse
      - saveSparse
      - to_sparse

  - title: Visualization
    desc: Plot LD matrices as heatmaps.
    contents:
      - plot_LD

  - title: VCF Utilities
    desc: VCF sample selection and format conversion.
    contents:
      - select_vcf_samples
      - vcf_to_plink

  - title: Allele Frequencies
    desc: Minor allele frequency retrieval.
    contents:
      - get_MAF_UKB

  - title: Bundled data
    contents:
      - popDat_1KGphase1
      - popDat_1KGphase3