_pkgdown.yml

destination: docs
url: https://nuno-agostinho.github.io/cTRAP/
template:
  params:
    ganalytics: UA-156449666-2
reference:
  - title: "Interactive functions"
    contents:
      - launchDiffExprLoader
      - launchCMapDataLoader
      - launchResultPlotter
      - launchMetadataViewer
      - launchDrugSetEnrichmentAnalyser
      - cTRAP
  - title: "Prepare ENCODE data"
    contents:
      - matches("ENCODE")
      - convertENSEMBLtoGeneSymbols
      - performDifferentialExpression
  - title: "Download and manipulate CMap perturbation data"
    contents:
      - getCMapConditions
      - getCMapPerturbationTypes
      - loadCMapData
      - loadCMapZscores
      - filterCMapMetadata
      - prepareCMapPerturbations
      - dim.perturbationChanges
      - dimnames.perturbationChanges
      - "`[.perturbationChanges`"
      - plot.perturbationChanges
      - parseCMapID
  - title: "Rank similar CMap perturbations"
    contents:
      - rankSimilarPerturbations
      - plot.referenceComparison
      - as.table.referenceComparison
      - plotTargetingDrugsVSsimilarPerturbations
      - print.similarPerturbations
  - title: "Predict targeting drugs"
    contents:
      - listExpressionDrugSensitivityAssociation
      - loadExpressionDrugSensitivityAssociation
      - dimnames.expressionDrugSensitivityAssociation
      - predictTargetingDrugs
      - plot.referenceComparison
      - as.table.referenceComparison
      - plotTargetingDrugsVSsimilarPerturbations
  - title: "Analyse drug (descriptor) set enrichment"
    contents:
      - loadDrugDescriptors
      - prepareDrugSets
      - analyseDrugSetEnrichment
      - plotDrugSetEnrichment
  - title: internal
    contents:
      - convertGeneIdentifiers