_pkgdown.yml

reference:
- title: "Primary Workflow"
  desc: "The primary building blocks of an analysis"
- subtitle: "Connecting to Data and Standards"
  desc: "Operations for starting an analyssis"
- contents:
  - process_mzroll
  - process_mzroll_multi
  - configure_db_access
- subtitle: "Processing and Normalization"
  desc: "Operations which modify the working data"
- contents:
  - normalize_peaks
  - floor_peaks
  - collapse_injections
  - filter_groupIds
- subtitle: "Statistics"
  desc: "Finding metabolites/lipids with interesting patterns of variability"
- contents:
  - diffex_mzroll
  - pathway_enrichments
- subtitle: "Plotting"
- contents:
  - starts_with("plot")
  - pvalue_histograms
  - volcano_plot
- subtitle: "Export"
- contents:
  - starts_with("write")
- title: "Advanced Methods"
  desc: "These methods are compatible with the standard workflow but have syntax which is too tricky for many users"
- contents:
  - filter_peakgroups_quo
  - filter_samples_quo
- title: "Dev Tools"
  desc: "Functions used behind the scenes"
- subtitle: "Sample Sheets"
- contents:
  - find_tracking_sheet
  - import_sample_sheet
  - read_sample_list
  - augment_samples_with_samplesheet
- subtitle: "Data Structures"
- contents:
  - aggregate_mzroll_nest
  - mzroll_table
  - test_mzroll_list
- subtitle: "Utils"
- contents:
  - calculate_pathway_enrichment
  - hclust_order
  - lipid_components
  - query_systematic_compounds
  - reconcile_mzroll_list
  - remove_constant_name
  - summarize_compound_pathways
  - X0106_paths
template:
  params:
    bootswatch: flatly