_pkgdown.yml

url: https://mglev1n.github.io/levinmisc/
template:
  bootstrap: 5
reference:

- title: Targets
  desc: Build a simple {targets} project
  contents:
  - has_concept("targets")

- title: Genomics
  desc: Genomics utility functions and wrappers around other tools/programs/packages to perform GWAS meta-analysis, fine-mapping, colocalization, and more.

- subtitle: Annotation
  desc: Functions that are useful for annotating GWAS summary statistics
  contents:
  - has_concept("annotation")

- subtitle: GWAS
  desc: Functions that are useful for performing GWAS/GWAS meta-analysis
  contents:
  - has_concept("GWAS meta-analysis")

- subtitle: Linkage disequilibrium
  desc: Functions that are useful for linkage disequilibrium
  contents:
  - has_concept("linkage disequilibrium")

- subtitle: Colocalization
  desc: >
    Functions that are useful for performing colocalization.
    Colocalization is a technique for evaluating the evidence supporting the presence of shared causal variant(s) at a given locus across two or more traits.
    Several methods of colocalization have been described, which generally leverage GWAS summary statistics across multiple traits.
    The methods use either proportional or enumeration approaches, which make different assumptions and test different hypotheses.
  contents:
  - has_concept("colocalization")

- subtitle: Finemapping
  desc: >
    Functions that are useful for finemapping.
    Finemapping is an approach for identifying the putative causal variant(s) at a locus identified in a GWAS.
    Like colocalization, finemapping methods make different assumptions about the configuration of causal variant(s) at the locus.
  contents:
  - has_concept("finemapping")

- subtitle: Heritability
  desc: >
    Functions that are useful for estimating heritability.
    Several tools for performing heritability estimation using GWAS summary statistics have been developed, including LDSC and LDAK.
    The [ldscr](https://mglev1n.github.io/ldscr/) package provides a native R implemtation of LDSC.
  contents:
  - has_concept("heritability")

- subtitle: TWAS/Gene-based testing
  desc: >
    Functions that are useful for identifying trait-associated genes from GWAS.
  contents:
  - has_concept("TWAS")
  - has_concept("Gene-based testing")

- title: Miscellaneous
  desc: Miscellaneous functions useful for manipulating/presenting data.
  contents:
  - has_concept("miscellaneous")
  - has_concept("plotting")
  - lacks_concepts(c("genomics", "targets"))