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

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url: https://zaoqu-liu.github.io/CellProgramMapper/
destination: docs

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

home:
  title: CellProgramMapper
  description: >
    Projection of Single-Cell Transcriptomic Data onto Reference Gene Expression Programs

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

navbar:
  structure:
    left:  [intro, reference, articles]
    right: [search, github]
  components:
    articles:
      text: Articles
      menu:
      - text: Getting Started
      - text: Quick Start Guide
        href: articles/quickstart.html
      - text: "---"
      - text: Algorithm & Theory
      - text: Mathematical Framework
        href: articles/algorithm.html
      - text: NNLS Solver Details
        href: articles/nnls-solver.html
      - text: "---"
      - text: Advanced Usage
      - text: Building Custom References
        href: articles/custom-reference.html
      - text: Visualization Guide
        href: articles/visualization.html

reference:
- title: Main Functions
  desc: Core functions for mapping cells to gene expression programs
  contents:
  - CellProgramMapper
  - get_usage
  - get_scores
  - print.CellProgramMapperResult
  - summary.CellProgramMapperResult

- title: Reference Management
  desc: Functions for managing reference datasets
  contents:
  - available_references
  - load_reference
  - download_reference
  - get_reference_names

- title: Consensus Reference Building
  desc: Build consensus GEPs from multiple cNMF results
  contents:
  - BuildConsensusReference
  - cluster_geps
  - pairwise_cluster_geps
  - compute_gep_correlations
  - get_top_genes_per_cgep
  - merge_spectra
  - merge_score_spectra
  - write_consensus_results

- title: Scoring
  desc: Compute add-on scores from usage matrix
  contents:
  - compute_scores
  - compute_external_score
  - create_score_definition
  - create_score_data

- title: Seurat Integration
  desc: Functions for Seurat object integration
  contents:
  - add_results_to_seurat
  - is_seurat
  - check_seurat_available
  - get_seurat_version
  - get_counts_from_seurat
  - get_cells_from_seurat
  - get_genes_from_seurat

- title: Data I/O
  desc: Data input/output functions
  contents:
  - load_counts
  - load_10x_mtx
  - load_h5ad
  - load_h5ad_hdf5r
  - load_text_matrix
  - load_tpm_stats
  - save_results
  - decompress_tar

- title: NMF Refitting
  desc: Core NNLS solver functions
  contents:
  - fit_usage
  - fit_usage_batched
  - prepare_query
  - scale_columns

- title: Utility Functions
  desc: Helper functions for data manipulation
  contents:
  - row_sums
  - col_sums
  - normalize_rows
  - is_integer_matrix
  - is_nonnegative_matrix
  - filter_na_genes
  - aggregate_by_cluster
  - ensure_dir
  - get_cache_dir
  - msg

- title: Internal
  desc: Internal functions (not for direct use)
  contents:
  - CellProgramMapper-package
  - consensus
  - io
  - mapper
  - nmf_refit
  - reference
  - scoring
  - seurat_compat
  - utils
  - zzz

footer:
  structure:
    left: developed_by
    right: built_with