_pkgdown.yml

url: https://january3.github.io/tmod/
template:
  bootstrap: 5
  bootswatch: zephyr
home:
  links:
  - text: User manual
    href: articles/user_manual/tmod_user_manual.html
  - text: View on github
    href: https://github.com/january3/tmod/
reference:
  - title: "Gene set enrichment tests and analyses"
  - contents:
    - tmodCERNOtest
    - tmodPCA
    - tmodSummary
    - tmodLEA
    - tmodLEASummary
    - tmodDecideTests
    - tmodLimmaTest
    - tmodLimmaDecideTests
    - tmodLimmaTopTable
    - tmodAUC
  - title: "Gene set (module) analysis"
  - contents:
    - eigengene
    - modGroups
    - modOverlaps
    - modcors
    - modjaccard
  - title: "Visualizations"
  - contents:
    - ggPanelplot
    - ggEvidencePlot
    - tmodPanelPlot
    - pvalEffectPlot
    - upset
    - evidencePlot
    - hgEnrichmentPlot
    - modCorPlot
    - showGene
    - pcaplot
    - tmodPal
    - tmodTagcloud
    - simplePie
  - title: "Creating and manipulating gene sets (modules)"
  - contents:
    - makeTmod
    - makeTmodFromDataFrame
    - tmodImportMSigDB
    - tmod2DataFrame
    - getGenes
    - getModuleMembers
    - showModule
    - tmod_ids
    - tmod2tmodGS
    - check_tmod_gs
  - title: "Data sets"
  - contents:
    - tmod-data
    - modmetabo
    - Egambia
    - EgambiaResults
    - vaccination
    - cell_signatures
    - tbmprof
  - title: "General and package classes"
  - contents:
    - tmod-package