_pkgdown.yml

home:
  title: An R package to enrich your differentially methylated region (DMR) analysis with the tidyverse
  description: DMRichR is an executable and R package for the statistical analysis and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports).

url: https://ben-laufer.github.io/DMRichR

development:
  mode: "release"
  
template:
  bootstrap: 5

reference:
  - title: Main function
    contents:
      - DM.R
  - title: Preprocessing
    contents:
      - processBismark
  - title: Annotations
    contents:
      - annotationDatabases
      - annotateRegions
      - DMReport
      - getCpGs
      - getExons
  - title: DMR plots
    contents:
      - plotDMRs2
      - smoothPheatmap
      - Manhattan
  - title: Global methylation
  - subtitle: Statistics
    contents:
      - globalStats
  - subtitle: Value extraction
    contents:
      - CGi
      - CpGs
      - windows
  - subtitle: Plots
    contents:
      - PCA
      - densityPlot
  - title: Enrichment testing
  - subtitle: Gene ontology
    contents:
      - GOfuncR
      - slimGO
      - GOplot
  - subtitle: Gene region and CpG 
    contents:
      - DMRichCpG
      - DMRichGenic
      - DMRichPlot
      - DMparseR
  - subtitle: Imprinting
    contents:
      - imprintOverlap
  - subtitle: Reference epigenomics
    contents:
      - chromHMM
      - chromHMM_heatmap
      - roadmap
      - roadmap_heatmap
  - subtitle: Transcription factor motifs
    contents:
      - prepareHOMER
      - HOMER
  - title: Machine learning
    contents:
      - methylLearn
  - title: Helper functions
    contents:
      - arrayLift
      - dmrList
      - extend
      - getBackground
      - gg_color_hue
      - gr2bed
      - read_excel_all
      - smooth2txt
  - title: Package
    contents:
      - DMRichR
      - .onAttach