bulkseqviz/_pkgdown.yml at master · MobinKhoramjoo/bulkseqviz · GitHub

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url: https://MobinKhoramjoo.github.io/bulkseqvis
template:
  bootstrap: 5

# Explicitly set developer/author for the sidebar
authors:
  Mobin Khoramjoo:
    href: https://github.com/MobinKhoramjoo
    roles: [aut, cre]

# Navigation Bar Setup
navbar:
  structure:
    left:  [intro, reference, articles, news]
    right: [search, github]
  components:
    reference:
      text: Functions
      href: reference/index.html
    articles:
      text: Vignette
      href: articles/workflow.html

# Organize functions into logical groups
reference:
  - title: "Data Import & Object Creation"
    desc: "Functions to set up the analysis object."
    contents:
      - create_bulkseqvis_object
      - print.bulkseq

  - title: "Quality Control"
    desc: "Visualizations for checking data quality and sample similarity."
    contents:
      - overall_count_boxplot
      - sample_distance_heatmap

  - title: "Dimensionality Reduction"
    desc: "Exploratory analysis using PCA, UMAP, and t-SNE."
    contents:
      - plot_pca_2d
      - plot_pca_3d
      - plot_umap_2d
      - plot_tsne_2d

  - title: "Differential Expression"
    desc: "Core analysis functions."
    contents:
      - DEG

  - title: "Results Visualization"
    desc: "Plots for interpreting differential expression results."
    contents:
      - plot_volcano
      - plot_deg_bar
      - plot_fcvsfc
      - plot_fc_dotplot
      - plot_gene_boxplot