pepdiff/_pkgdown.yml at master · TeamMacLean/pepdiff · GitHub

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url: https://teammaclean.github.io/pepdiff/

template:
  bootstrap: 5
  bootswatch: flatly

navbar:
  structure:
    left: [intro, reference, articles]
    right: [search, github]
  components:
    articles:
      text: Articles
      menu:
      - text: Getting Started
        href: articles/basic_workflow.html
      - text: "---"
      - text: Analysis Methods
      - text: GLM Analysis
        href: articles/glm_analysis.html
      - text: ART Analysis
        href: articles/art_analysis.html
      - text: Pairwise Tests
        href: articles/pairwise_tests.html
      - text: "---"
      - text: Diagnostics
      - text: Checking Model Fit
        href: articles/checking_fit.html
      - text: Diagnostic Plots
        href: articles/diagnostic_plots.html

reference:
- title: Import & Data
  desc: Import data and create pepdiff_data objects
  contents:
  - read_pepdiff
  - combine_tech_reps
  - import_data
  - new_pepdiff_data
  - validate_pepdiff_data
  - print.pepdiff_data
  - summary.pepdiff_data
  - subset.pepdiff_data
  - plot.pepdiff_data

- title: Analysis
  desc: Run differential abundance analysis
  contents:
  - compare
  - compare_glm
  - compare_art
  - compare_pairwise
  - compare_pairwise_rankprod
  - compare_within_strata
  - significant
  - get_peptide
  - get_comparison

- title: Results

  desc: Results class and methods
  contents:
  - new_pepdiff_results
  - validate_pepdiff_results
  - print.pepdiff_results
  - summary.pepdiff_results
  - plot.pepdiff_results
  - long_results
  - build_results_tibble
  - build_pairwise_results

- title: Diagnostics
  desc: Check model fit and convergence
  contents:
  - plot_fit_diagnostics
  - extract_diagnostics
  - extract_stored_residuals
  - get_all_residuals
  - print_diagnostic_summary

- title: Visualization
  desc: Plot functions for data and results
  contents:
  - plot_pca
  - plot_pca_simple
  - plot_heatmap
  - plot_volcano_new
  - plot_volcano_bf
  - plot_pvalue_histogram
  - plot_fc_distribution_new
  - plot_bf_distribution
  - plot_distributions_simple
  - plot_missingness_simple
  - plot_quant_distributions
  - plot_fc
  - plot_kmeans
  - plot_result
  - volcano_plot
  - p_value_hist
  - fc_qqplot
  - norm_qqplot
  - missing_peptides_plot
  - times_measured_plot

- title: Statistical Tests
  desc: Individual test implementations
  contents:
  - test_wilcoxon
  - test_bootstrap_t
  - test_bayes_t
  - test_rankprod
  - jzs_bf_approx
  - classify_bf_evidence
  - calc_t_statistic
  - calc_rank_product
  - build_replicate_matrix

- title: Model Fitting
  desc: GLM and ART model fitting internals
  contents:
  - fit_glm
  - fit_art
  - fit_and_extract_glm
  - fit_and_extract_art
  - extract_contrasts_glm
  - extract_contrasts_art
  - run_models
  - has_sufficient_variation
  - build_formula

- title: Data Utilities
  desc: Helper functions for data manipulation
  contents:
  - assess_missing
  - compute_missingness
  - compute_design_summary
  - times_measured
  - fold_change_matrix
  - matrix_data
  - list2mat
  - mean_fold_change
  - log2_fc
  - apply_fdr_by_comparison

- title: Legacy Functions
  desc: Deprecated functions from earlier versions
  contents:
  - compare.data.frame
  - compare_legacy
  - compare_many
  - compare_calls
  - get_sig_rows
  - estimate_result_clusters
  - kmeans_by_selected_cols
  - get_bootstrap_percentile
  - get_wilcoxon_percentile
  - get_kruskal_percentile
  - get_rp_percentile
  - get_percentile_lowest_observed_value_iterative
  - select_columns_for_contrast
  - min_peptide_values
  - replace_vals
  - metrics

- title: Internal Utilities
  desc: Internal helper functions
  contents:
  - validate_factors
  - validate_positive
  - check_zeros
  - is_useable

home:
  links:
  - text: peppwR (companion package)
    href: https://github.com/TeamMacLean/peppwR