_pkgdown.yml

reference:
  - title: "Data import"
    desc: >
      Functions for importing external data and converting other R object
      as phyloseq or reverse converting
    contents:
      - starts_with("import")
      - import_biom
      - phyloseq2DESeq2
      - phyloseq2edgeR
      - phyloseq2metagenomeSeq
      - otu_table2metagenomeSeq
  - title: "Microbiome marker"
    desc: S4 class and methods for microbiomeMarker
    contents:
      - microbiomeMarker
      - starts_with("microbiomeMarker-class")
      - marker_table-class
      - marker_table
      - marker_table<-
      - assign-otu_table
      - abundances
      - nmarker
      - "["
      - starts_with("postHocTest-class")
      - postHocTest
      - extract_posthoc_res
  - title: Functions reexports from phyloseq
    contents: reexports
      # - nsamples
      # - ntaxa
      # - otu_table
      # - sample_data
      # - sample_names
      # - tax_table
      # - taxa_names
  - title: "Normalization"
    contents:
      - abundances
      - transform_abundances
      - starts_with("norm")
  - title: "Differential analysis"
    desc: Functions for identifying the microbiome markers
    contents:
      - confounder
      - starts_with("run")
  - title: "Comparison of different methods"
    contents: 
      - compare_DA
      - summary.compareDA
  - title: "Visualization"
    contents:
      - starts_with("plot")
  - title: "Example data"
    contents:
      starts_with("data")
  - title: Miscellaneous
    contents:
      - aggregate_taxa
      - subset_marker
      - summarize_taxa