multideconv/_pkgdown.yml at main · VeraPancaldiLab/multideconv · GitHub

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url: https://verapancaldilab.github.io/multideconv/
template:
  bootstrap: 5
  bslib:
    pkgdown-nav-height: 100px

home:
  sidebar:
    structure: [links, license, community, citation, authors, dev, toc]

navbar:
  structure:
    left:  [intro, articles, reference, news]
    right: [search, github]
  components:
    articles:
      text: Articles
      menu:
      - text: "Deconvolution with default methods"
        href: articles/a1_deconvolution.html
      - text: "Single-cell deconvolution"
        href: articles/a2_single_cell.html
      - text: "Pseudo-bulk profiles and benchmarking"
        href: articles/a3_benchmark.html
      - text: "Cell type subgroup analysis"
        href: articles/a4_subgroups.html
      - text: "Machine learning workflows"
        href: articles/a5_machine_learning.html

articles:
- title: "Tutorial"
  contents:
  - a1_deconvolution
  - a2_single_cell
  - a3_benchmark
  - a4_subgroups
  - a5_machine_learning

reference:
- title: Main
  desc: >
    Public user-facing functions
  contents:
  - compute.deconvolution
  - compute.deconvolution.analysis
  - replicate_deconvolution_subgroups
  - compute_deconvolution_dictionary
  - compute_subgroups_pathways
  - estimate_expression_profiles
  - prepare_multideconv_folds
- title: Benchmarking
  desc: >
    Public benchmarking workflow
  contents:
  - compute.benchmark
- title: Single cell functions
  desc: >
    Public single-cell utilities
  contents:
  - create_metacells
  - create_sc_pseudobulk
  - create_sc_signatures
- title: Utils
  desc: >
    Internal use (not exported functions)
  contents:
  - standardize_celltype_colnames
  - compute.deconvolution.preprocessing
  - compute_methods_variable_signature
  - compute_sc_deconvolution_methods
  - deconvolution_dictionary
  - compute_data_driven_rank
  - create_gsea_signature
  - computeCBSX
  - computeCBSX_parallel
  - computeDWLS
  - computeDWLS_parallel
  - computeDeconRNASeq
  - computeEpiDISH
  - computeMCP
  - computeMOMF
  - computeMOMF_parallel
  - computeQuantiseq
  - computeXCell
  - compute_subgroups
  - compute.cell.types
  - corr_subgroups
  - remove_subgroups
  - remove_low_variance
  - find.maximum.iteration
  - removeCorrelatedFeatures
- title: Package Data
  desc: >
    Example data
  contents:
  - raw_counts
  - deconv_bulk
  - deconvolution
  - metacells_data
  - metacells_metadata
  - pseudobulk
  - cells_groundtruth
  - subgroups
  - sample_labels
  - cell_labels