spatialecotyper/_pkgdown.yml at main · digitalcytometry/spatialecotyper · GitHub

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url: https://digitalcytometry.github.io/spatialecotyper

development:
  mode: auto

repo:
  url:
    home: https://github.com/digitalcytometry/spatialecotyper
    source: https://github.com/digitalcytometry/spatialecotyper/blob/main/
    issue: https://github.com/digitalcytometry/spatialecotyper/issues
  branch: main

template:
  bootswatch: simplex
  bootstrap: 5
  bslib:
    primary: "#0054AD"
    border-radius: 0.5rem
    btn-border-radius: 0.25rem

authors:
  Wubing Zhang:
    href: https://profiles.stanford.edu/wubing-zhang
  Aaron Newman Lab:
    href: https://anlab.stanford.edu/

navbar:
  title: ~
  type: default
  left:
    - text: Vignettes
      menu:
      - text: Discovering Spatial Ecotypes from a Single Spatial Transcriptomics Sample
        href: articles/SingleSample.html
      - text: Discovering Conserved Spatial Ecotypes Across Multiple Spatial Transcriptomics Samples
        href: articles/Integration.html
      - text: Identifying SE-Specific Cell States via Leave-One-Sample-Out Cross-Validation
        href: articles/Discovery_SE_CellStates.html
      - text: NMF Model Development for Spatial Ecotype Recovery from Single-Cell and Spatial Transcriptomics Data
        href: articles/TrainRecoveryModel.html
      - text: Recovering Spatial Ecotypes from Single-Cell Spatial Transcriptomics Data
        href: articles/Recovery_scST.html
      - text: Recovering Spatial Ecotypes from Single-Cell RNA-seq Data
        href: articles/Recovery_scRNA.html
      - text: NMF Model Development for Spatial Ecotype Deconvolution from Bulk Gene Expression Data
        href: articles/TrainDeconvModel.html
      - text: Inferring Spatial Ecotype Abundances from Bulk Gene Expression Data
        href: articles/Recovery_Bulk.html

    - text: R functions
      href: reference/index.html
    - text: News
      href: news/index.html

reference:
- title: Discovering Spatial Ecotypes
  contents:
  - SpatialEcoTyper
  - MultiSpatialEcoTyper
  - IntegrateSpatialEcoTyper
  - GetSpatialMetacells
  - ComputeFCs
  - SNF2
  - GetPCList
  - getSN
  - GetSNList
  - Integrate

- title: Identifying SE-Specific Cell States
  desc: Identifying SE-specific cell states via leave-one-sample-out cross-validation.
  contents:
  - LoocvPredict
  - ComputeMetrics

- title: NMF Model Development for Spatial Ecotype Recovery and Deconvolution
  desc:  Developing NMF models for recovering spatial ecotypes from single-cell spatial data, scRNA-seq data, Visium spatial data, or bulk tumor expression data.
  contents:
  - CreatePseudobulks
  - NMFGenerateW
  - NMFGenerateWList

- title: Recovering Spatial Ecotypes
  desc:  Recovering spatial ecotypes from single-cell spatial transcriptomics, scRNA-seq, Visium, or bulk tumor expression data.
  contents:
  - RecoverSE
  - DeconvoluteSE
  - NMFpredict

- title: Validating Spatial Ecotypes
  desc:  Validating spatial ecotypes in held-out single-cell or spatial transcriptomics data by testing the co-association or spatial autocorrelation of recovered SE-specific cell states.
  contents:
  - Colocalization
  - ColocalizationHeatmapView
  - CoassociationTest
  - Coassociation
  - ComputeNormalizedMoranI
  - AverageConsensusMarkers

- title: Clustering Analysis
  desc:  Clustering via NMF.
  contents:
  - nmfClustering

- title: Visualization
  contents:
  - SpatialView
  - HeatmapView
  - drawRectangleAnnotation
  - getColors

- title: Data Processing
  contents:
  - PreprocessST
  - AnnotateCells
  - Znorm
  - rankSparse
  - matrixMultiply
  - fillspots
  - mostFrequent

news:
  releases:
  - text: "Version 1.0.2"
    href: