ProjectSVR/_pkgdown.yml at main · JarningGau/ProjectSVR · GitHub

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url: jarninggau.github.io/ProjectSVR/

destination: docs

template:
  params:
    bootswatch: flatly

navbar:
  structure:
    left: [home, tutorials, reference, news]
    right: [github]
  components:
    tutorials:
      text: Tutorials
      menu:
      - text: Generic example
      - text: Quick start
        href: articles/quick_start.html
      - text: ------------
      - text: Build reference model
      - text: DISCO blood atlas
        href: articles/model_pbmc.html
      - text: Maternal-fetal interface atlas
        href: articles/model_mfia.html
      - text: Pan-cancer T cell lanscape
        href: articles/model_pctl.html
      - text: Mouse testicular cell atlas
        href: articles/model_mtca.html
      - text: ------------
      - text: Map query dataset
      - text: Decidual immune microenvironment of RPL patients
        href: articles/mapQuery_immune_RPL.html
      - text: ICB responsiveness of BRCA
        href: articles/mapQuery_ICB_BRCA.html
      - text: Genetic perturbed germ cells (Zfp541-KO)
        href: articles/mapQuery_Zfp541-KO.html
      - text: Genetic perturbed germ cells (Ythdc2-KO)
        href: articles/mapQuery_Ythdc2-KO.html
      - text: In vitro induced meiosis
        href: articles/mapQuery_invitro_meiosis.html
      - text: ------------
      - text: MISC
      - text: Training the reference pseudotime model
        href: articles/misc_Ythdc2-KO_pseudotime.html
      - text: Training the SVM model for cell type prediction
        href: articles/misc_disco_pbmc_svm.html

reference:
- title: "Class"
  desc: "Class defined in ProjectSVR"
- contents:
  - has_concept("class")

- title: "Object interaction"
  desc: "Functions for interacting with objects in ProjectSVR"
- contents:
  - has_concept("object")

- title: "Meta cell"
  desc: "Functions for making meta cells"
- contents:
  - has_concept("meta_cell")

- title: "Feature selection"
  desc: "Functions for extract signature gene sets"
- contents:
  - has_concept("extract_signature")

- title: "Gene module score"
  desc: "Functions for computing gene module score"
- contents:
  - has_concept("compute_module_score")


- title: "Reference model construction"
  desc: "Functions for training reference model"
- contents:
  - has_concept("training_model")

- title: "Reference mapping"
  desc: "Functions for reference mapping"
- contents:
  - has_concept("reference_mapping")

- title: "Label transfer"
  desc: "Functions for label transfer"
- contents:
  - has_concept("label_transfer")

- title: "Differential cell population"
  desc: "Functions for testing differential cell population"
- contents:
  - has_concept("differential_population")

- title: "Visualization"
  desc: "Functions for nice plots"
- contents:
  - has_concept("plot")

- title: "Data"
  desc: "Descriptions of data included with ProjectSVR"
- contents:
  - has_concept("data")

- title: "Internal"
  desc: "Internal functions"
- contents:
  - has_concept("internal")