FastCCCR/_pkgdown.yml at main · WaveoffBioMed/FastCCCR · GitHub

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url: https://zaoqu-liu.github.io/FastCCCR/

template:
  bootstrap: 5
  bootswatch: flatly
  bslib:
    primary: "#0d6efd"
    border-radius: 0.5rem
    btn-border-radius: 0.25rem

home:
  title: FastCCCR - Fast Cell-Cell Communication Analysis
  description: >
    High-performance R package for cell-cell communication inference
    in single-cell RNA sequencing data with statistical framework.

authors:
  Zaoqu Liu:
    href: https://github.com/Zaoqu-Liu

navbar:
  structure:
    left:  [intro, reference, articles]
    right: [search, github]
  components:
    articles:
      text: Tutorials
      menu:
      - text: Getting Started
        href: articles/quick-start.html
      - text: Algorithm Details
        href: articles/algorithm.html
      - text: Reference-Based Inference
        href: articles/reference-based.html
      - text: Visualization Gallery
        href: articles/visualization.html

articles:
- title: Tutorials
  navbar: ~
  contents:
  - quick-start
  - algorithm
  - reference-based
  - visualization

reference:
- title: Core Analysis Functions
  desc: Main functions for CCC analysis
  contents:
  - fastccc
  - fastccc_cauchy
  - statistical_analysis_method
  - cluster_markers_method
  - create_significant_df
  - core

- title: Reference-Based Inference
  desc: Functions for building and using reference panels
  contents:
  - build_reference
  - infer_query
  - load_reference_config
  - starts_with("build-reference")
  - starts_with("infer-query")

- title: Distribution Operations
  desc: Statistical distribution classes and functions
  contents:
  - Distribution
  - create_distribution
  - get_pvalue
  - get_threshold
  - get_minimum_distribution
  - get_pmf_from_digit_samples
  - get_average_distribution
  - combine_complex_distribution_dt
  - starts_with("dist-")

- title: Score Calculation
  desc: Functions for expression score computation
  contents:
  - calculate_cluster_mean
  - calculate_cluster_percents
  - calculate_cluster_quantile
  - calculate_interactions_strength
  - combine_complex_distribution
  - analyze_interactions_percents
  - score

- title: P-value Computation
  desc: Functions for statistical inference
  contents:
  - calculate_cluster_mean_distribution
  - calculate_cluster_quantile_distribution
  - calculate_interactions_pvalue
  - check_interactions_by_DEG
  - cauchy_combine
  - cauchy_combine_files
  - cauchy_combine_with_stat
  - starts_with("cauchy-combine")

- title: Data Preprocessing
  desc: Functions for data loading and preprocessing
  contents:
  - get_input_data
  - get_interactions
  - get_count_data
  - get_input_data_from_files
  - starts_with("data-preprocess")

- title: Visualization
  desc: Plotting functions
  contents:
  - plot_ccc_network
  - plot_ccc_heatmap
  - plot_ccc_chord
  - get_network_data
  - get_strength_network_data
  - visualize

- title: C++ Functions
  desc: Low-level C++ implementations
  contents:
  - ends_with("_cpp")

- title: Package
  desc: Package documentation
  contents:
  - FastCCCR-package
  - utils

footer:
  structure:
    left: developed_by
    right: built_with