_pkgdown.yml

url: https://zhanglabgt.github.io/scMultiSim/
template:
  bootstrap: 5
  light-switch: true
articles:
  - title: Tutorials
    navbar: ~
    contents:
      - workflow
      - basics
      - spatialCCI
      - options
reference:
  - title: Simulation
    desc: Functions for simulating single-cell data.
  - contents:
      - sim_true_counts
      - add_expr_noise
      - divide_batches
      - add_outliers
  - title: Visualization
    desc: Functions for visualizing the results.
  - contents:
    - starts_with("plot_")
    - gene_corr_cci
    - gene_corr_regulator
  - title: Help
    desc: Functions for getting help.
  - contents:
    - run_shiny
    - scmultisim_help
  - title: Utilities
    desc: Utility functions that can be useful for simulating data.
  - contents:
    - cci_cell_type_params
    - gen_clutter
  - title: Data
    desc: Default data provided by scMultiSim
  - contents:
    - starts_with("Phyla")
    - has_keyword("datasets")
  - title: Internal helpers
    desc: Internal helper functions, but can be useful for advanced customization.
  - contents:
    - Get_1region_ATAC_correlation
    - Get_ATAC_correlation
    - True2ObservedATAC
    - True2ObservedCounts
    - sim_example_200_cells
    - sim_example_200_cells_spatial