_pkgdown.yml

url: https://liaoyjruby.github.io/Rubrary/
template:
  bootstrap: 5
  bootswatch: flatly
  theme: arrow-light
  bslib:
    primary: '#6F1A07'
    secondary: '#e77575'

reference:
  - title: Exploratory data analysis
    contents:
      - plot_distribution
      - plot_density
      - plot_scatter
      - get_kspval
      - check_normal
      - calc_sumZscore
      - run_RRHO
      - phyper_df
  - title: Principal components analysis (PCA)
    contents:
      - run_PCA
      - plot_PCA
      - plot_PCA_matrix
      - plot_PCA_3D
      - plot_PCA_biplot
      - get_loadings
      - plot_screeplot
      - rotate_varimax
      - predict_PCA
  - title: Differentially expressed genes (DESeq)
    contents:
      - output_DESeq
      - plot_DEgene_boxplot
      - plot_waterfall
      - plot_volcano
  - title: Gene set enrichment analysis (GSEA)
    desc: Including GSEA Squared functions.
    contents:
      - format_GSEA_name
      - plot_GSEA_barplot
      - plot_GSEA_pathway
      - plot_GSEA_pathway_batch
      - get_GSEAsq_terms
      - run_GSEA_squared
      - plot_GSEAsq_density
  - title: Single cell RNA analysis
    desc: Seurat object based analysis and visualization.
    contents:
      - plot_dimplot_grid
      - plot_comp_barplot
      - plot_featurescatter
      - assess_integration
      - run_LISI
      - run_MixingMetric
      - run_CellMixS
      - genecoexp_scatter_hyper
  - title: Gene manipulation
    contents:
      - convert_genes
      - get_PC_genes
      - filter_genes
      - get_gene_desc
      - quantile_norm
      - get_log_coding_geneexp
  - title: Utility
    desc: Miscellaneous helper functions.
    contents:
      - rread
      - rwrite
      - corner
      - split_line
      - full_join_rownames
      - left_join_rownames
      - cbind.fill
      - use_pkg
      - inst_pkg
      - reload_pkg
  - title: Data
    desc: Used for vignettes and examples.
    contents:
      - airway_deseq_res
      - GSEA_pathways