_pkgdown.yml

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: Core
      - text: Cell type deconvolution and interaction analysis
        href: articles/visium_BC.html
      - text: Deconvolution with a matched scRNA-seq data set
        href: articles/oldST_PDAC.html
      - text: Application to high resolution spatial transcriptomics data
        href: articles/hiresST_CRC.html
      - text: ----
      - text: Misc
      - text: Gene set score calculation for spatial spots
        href: articles/GeneSetScore.html
    - text: News
      href: news/index.html

reference:
  - title: SpaCET object
    contents:
    - SpaCET-class
    - create.SpaCET.object
    - create.SpaCET.object.10X
    - SpaCET.quality.control
    - SpaCET.quality.control
    - SpaCET.quality.control
    - convert.Seurat
    - addTo.Seurat

  - title: Deconvolution of ST data
    contents:
    - SpaCET.deconvolution
    - SpaCET.deconvolution.malignant
    - SpaCET.deconvolution.matched.scRNAseq
    - SpaCET.deconvolution.malignant.customized.scRNAseq

  - title: Cell-cell interaction analysis
    contents:
    - SpaCET.CCI.colocalization
    - SpaCET.CCI.LRNetworkScore
    - SpaCET.CCI.cellTypePair

  - title: Tumor-Stroma Interface
    contents:
    - SpaCET.identify.interface
    - SpaCET.combine.interface
    - SpaCET.distance.to.interface

  - title: Visualization
    contents:
    - SpaCET.visualize.spatialFeature
    - SpaCET.visualize.colocalization
    - SpaCET.visualize.cellTypePair

  - title: Gene set score calculation
    contents:
    - SpaCET.GeneSetScore
    - read.gmt
    - write.gmt