simxQTL/_pkgdown.yml at main · StatFunGen/simxQTL · GitHub

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url: https://statfungen.github.io/simxQTL

template:
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  math-rendering: katex
  bslib:
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development:
  mode: auto

home:
  links:
  - text: Learn more
    href: https://github.com/StatFunGen/simxQTL
  - text: Report a bug
    href: https://github.com/StatFunGen/simxQTL/issues

navbar:
  structure:
    left: [reference, articles, news]
    right: [search, github, lightswitch]
  components:
    reference:
      icon: fa fa-file-code
      text: Functions
      href: reference/index.html
      aria-label: Function reference
    articles:
      icon: fa fa-book-reader
      text: Vignettes
      href: articles/index.html
      aria-label: Articles and vignettes
    news:
      icon: fa fa-newspaper
      text: News
      href: news/index.html
      aria-label: Package news
    github:
      icon: fab fa-github
      href: https://github.com/StatFunGen/simxQTL
      aria-label: View source on GitHub

reference:
  - title: "Genotype Simulation"
    desc: "Functions for simulating genotype data"
    contents:
      - sim_geno_indep
      - sim_geno_LD
      - sim_geno_real

  - title: "Effect Size and Trait Simulation"
    desc: "Functions for simulating effect sizes and phenotypes"
    contents:
      - parse_num_causal_snps
      - sim_beta
      - sim_beta_fix_variant
      - simulate_polygenic_trait
      - sim_multi_traits
      - sim_single_trait_simple
      - simulate_phenotype

  - title: "Summary Statistics"
    desc: "Functions for simulating and calculating summary statistics"
    contents:
      - sim_sumstats
      - calculate_sumstat
      - get_correlation

  - title: "Cis-QTL Simulation"
    desc: "Functions for simulating cis-eQTL data, originally developed for the \"susieR 2.0\" manuscript, McCreight et al (2025)"
    contents:
      - generate_cis_qtl_data

  - title: "Trans-QTL Simulation"
    desc: "Functions for simulating trans-QTL and gene regulatory networks, originally developed for the \"transBoost\" manuscript, Cao et al (2026)"
    contents:
      - simulate_trans_expression
      - simulate_trans_mixture_celltype
      - get_random_A
      - gene_data
      - gene_data_null1
      - gene_data_null2
      - gene_data_null3

  - title: "Enrichment Analysis"
    desc: "Functions for simulating causal enrichment"
    contents:
      - simulate_causal_config

  - title: "Utility Functions"
    desc: "Helper functions for calculations"
    contents:
      - compute_s2g
      - get_lower_chol

articles:
  - title: "Phenotype Simulation"
    desc: "Tutorials for simulating phenotypes with various genetic architectures"
    contents:
    - sparse_phenotype_simulation
    - cis_qtl_simulation

footer:
  structure:
    left: developed_by
    right: built_with