_pkgdown.yml

---
url: https://insightsengineering.github.io/hermes

template:
  bootstrap: 5
  params:
    bootswatch: cerulean
    ganalytics: "UA-125641273-1"

navbar:
  right:
    - icon: fa-github
      href: https://github.com/insightsengineering/hermes

reference:
  - title: Package
    contents:
      - hermes-package
  - title: Classes
    contents:
      - HermesData
      - RangedHermesData
      - HermesDataCor
      - HermesDataPca
      - HermesDataTopGenes
      - HermesDataSummary
      - HermesDataPcaCor
      - HermesDataDiffExpr
      - ConnectionBiomart
      - GeneSpec
  - title: Constructors
    contents:
      - HermesData
      - HermesDataFromMatrix
      - gene_spec
  - title: Internal Helper Functions
    contents:
      - all_na
      - cat_with_newline
      - validate_counts
      - validate_cols
      - validate_row_data
      - validate_col_data
      - validate_names
      - validate_prefix
      - h_map_pos
      - h_rpkm
      - h_cpm
      - h_tpm
      - h_voom
      - h_low_expression_flag
      - h_low_depth_flag
      - h_tech_failure_flag
      - h_diff_expr_voom
      - h_diff_expr_deseq2
      - h_pca_var_rsquared
      - h_pca_df_r2_matrix
      - h_get_annotation_biomart
      - h_get_granges_by_id
      - h_get_size_biomart
      - h_ensembl_to_entrez_ids
      - h_strip_prefix
      - h_has_req_annotations
      - h_short_list
      - h_parens
      - h_all_duplicated
      - h_unique_labels
      - h_df_factors_with_explicit_na
      - h_draw_boxplot_df
  - title: Example Data
    contents:
      - expression_set
      - hermes_data
      - summarized_experiment
      - multi_assay_experiment
  - title: Methods
    contents:
      - annotation
      - cbind
      - correlate
      - counts
      - extra_data_names
      - filter
      - genes
      - isEmpty
      - lapply
      - metadata
      - normalize
      - prefix
      - query
      - rbind
      - rename
      - samples
      - show
      - subset
      - summary
  - title: Functions
    contents:
      - add_quality_flags
      - calc_pca
      - diff_expression
      - set_tech_failure
      - top_genes
      - connect_biomart
      - df_cols_to_factor
      - colPrinComp1
      - colMeanZscores
      - wrap_in_mae
      - col_data_with_genes
      - inner_join_cdisc
      - cut_quantile
  - title: Graphs
    contents:
      - draw_libsize_hist
      - draw_libsize_qq
      - draw_libsize_densities
      - draw_nonzero_boxplot
      - draw_genes_barplot
      - draw_heatmap
      - draw_scatterplot
      - draw_barplot
      - draw_boxplot
      - plot_all
  - title: Control Functions
    contents:
      - control_normalize
      - control_quality
  - title: Assertions
    contents:
      - assertion_arguments
      - check_proportion
      - is_class
      - is_counts_vector
      - is_hermes_data
      - is_list_with
      - is_constant
  - title: Constants
    contents:
      - .row_data_annotation_cols