_pkgdown.yml

url: https://biocor.llrs.dev
development:
  mode: auto

home:
  title: Calculate functional similarities between genes
  description: Calculates functional similarities based on the
    pathways or gene sets. These similarities can be calculated for pathways or
    gene sets, genes, or clusters and combined with other similarities. They
    can be used to improve networks, gene selection, testing relationships...

template:
  bootstrap: 5
  opengraph:
    image:
      src: man/figures/logo.png
      alt: "BioCor logo"
    twitter:
      creator: "@Lluis_Revilla"
      card: summary_large_image
twitterImg: man/figures/logo.png
reference:
  - title: General introduction
    contents:
    - BioCor-package
  - title: Similarity of pathways
    desc:  Compare pairs of pathways, just one (pathSim) or as many as you want (mpathSim)
    contents:
    - pathSim
    - mpathSim
  - title: Similarity of genes
    desc:  Compare pairs of genes, just one (geneSim) or as many as you want (mgeneSim)
    contents:
    - geneSim
    - mgeneSim
  - title: Pooling similarity of groups of genes
    desc:  Compare groups of genes by pooling all the pathways they are in
    contents:
    - clusterSim
    - mclusterSim
  - title: Similarity of groups of genes
    desc:  Compare groups of genes by comparing the similarity of the genes in each group
    contents:
    - clusterGeneSim
    - mclusterGeneSim
  - title: Convert between similarities
    desc: Convert from Jaccard to Dice or vice versa
    contents:
    - D2J
    - J2D
  - title: Combine similarities
    contents:
    - combineScores
    - combineScoresPar
  - title: Helper functions
    contents:
    - plot_data
    - combineSources
    - AintoB
    - seq2mat
    - combinadic
    - diceSim
    - duplicateIndices
    - removeDup
    - inverseList
    - similarities
    - addSimilarities
    - weighted.sum
    - weighted