_pkgdown.yml

url: https://klugerlab.github.io/MOSAIC/

template:
  bootstrap: 5

navbar:
  structure:
    left:  [home, reference, articles]
    right: [github]
  components:
    reference:
      text: Functions
      href: reference/index.html
    github:
      icon: fa-github
      href: https://github.com/KlugerLab/MOSAIC

reference:
  - title: "Core Embedding"
    desc: "Run the MOSAIC spectral co-embedding pipeline"
    contents:
      - run_MOSAIC
      - find_elbow_kneedle

  - title: "Differential Connectivity"
    desc: "Test for features with rewired regulatory networks across conditions"
    contents:
      - run_DC_test
      - calculate_empirical_pvalue

  - title: "Subgroup Detection"
    desc: "Identify patient subtypes from feature module connectivity"
    contents:
      - compute_module_similarity
      - find_partition_hclust

  - title: "Simulation"
    desc: "Generate synthetic multi-modal data for benchmarking"
    contents:
      - simulate_multimodal_data

  - title: "Visualization"
    desc: "Plot eigenvalue spectra and sample embeddings"
    contents:
      - plot_eigen
      - plot_mds_cluster