_pkgdown.yml

url: https://microbialgenomics-irsicaixaorg.github.io/dar/
template:
  bootstrap: 5
  bootswatch: minty
reference:
- title: "Basic Functions"
  contents:
  - dar
  - recipe
  - prep
  - bake
  - cool
- title: "Step Functions - Data Preprocessing"
  contents:
  - step_filter_taxa
  - step_filter_by_prevalence
  - step_filter_by_abundance
  - step_filter_by_rarity
  - step_filter_by_variance
  - step_subset_taxa
  - step_rarefaction
- title: "Step Functions - Differential Abundance Methods"
  contents:
  - step_aldex
  - step_ancom
  - step_corncob
  - step_deseq
  - step_lefse
  - step_maaslin
  - step_metagenomeseq
  - step_wilcox 
- title: "Exploration"
  contents:
  - abundance_plt
  - corr_heatmap
  - exclusion_plt
  - find_intersections
  - intersection_df
  - intersection_plt
  - mutual_plt
  - overlap_df
- title: "Recipe Getters and Adders"
  contents:
  - add_tax
  - add_var
  - get_phy
  - get_tax
  - get_var
  - otu_table
  - phy_qc
  - sample_data
  - steps_ids
  - tax_table
  - required_deps
  - zero_otu
- title: "Import and Export"
  contents:
  - export_steps
  - import_steps
  - read_data
- title: "Other functions"
  contents:
  - contains_rarefaction
  - rand_id
  - PrepRecipe-class
  - phyloseq_or_null-class
- title: "Data"
  contents:
  - metaHIV_phy
  - pastry_df
  - test_rec
  - test_prep_rec