SecAct/_pkgdown.yml at main · data2intelligence/SecAct · GitHub

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url: ~
template:
  bootstrap: 5

navbar:
  left:
    - icon: fas fa-home fa-lg
      href: index.html
    - text: Reference
      href: reference/index.html
    - text: Tutorials
      menu:
      - text: Spatial data
      - text: Signaling patterns and velocities for multi-cellular ST data
        href: articles/stPattern.html
      - text: Intercellular communication for single-cell resolution ST data
        href: articles/stCCC.html
      - text: Application to sub-cellular ST data
        href: articles/stSub.html
      - text: ----
      - text: Single-cell data
      - text: Secreted protein signaling activity for various cell states
        href: articles/scState.html
      - text: Cell-cell communication mediated by secreted proteins
        href: articles/scCCC.html
      - text: ----
      - text: Bulk data
      - text: Clinical relevance of secreted proteins in a large patient cohort
        href: articles/bulkCohort.html
      - text: Secreted protein activity change between two phenotypes
        href: articles/bulkChange.html
      - text: ----
      - text: Miscellaneous
      - text: Activity inference accelerators and batch mode
        href: articles/accelerator.html
    - text: News
      href: news/index.html

reference:
  - title: Activity inference
    contents:
    - SecAct.activity.inference
    - SecAct.activity.inference.ST
    - SecAct.activity.inference.scRNAseq

  - title: Downstream application
    contents:
    - SecAct.signaling.pattern
    - SecAct.signaling.pattern.gene
    - SecAct.signaling.velocity.spotST
    - SecAct.signaling.velocity.scST
    - SecAct.CCC.scST
    - SecAct.CCC.scRNAseq
    - SecAct.coxph.regression

  - title: Visualization
    contents:
    - SecAct.CCC.heatmap
    - SecAct.CCC.circle
    - SecAct.CCC.sankey
    - SecAct.CCC.dot
    - SecAct.heatmap.plot
    - SecAct.bar.plot
    - SecAct.lollipop.plot
    - SecAct.survival.plot