_pkgdown.yml

title: "scDiagnostics"

url: https://ccb-hms.github.io/scDiagnostics/

pandoc: 3.1.11
pkgdown: 2.1.0
pkgdown_sha: ~
last_built: 2024-08-24T18:56Z

template:
  params:
    bootswatch: flatly

navbar:
  title: "scDiagnostics"
  type: default
  left:
    - text: Vignettes
      menu:
        - text: Getting Started with scDiagnostics
          href: articles/scDiagnostics.html
        - text: Visualization of Cell Type Annotations
          href: articles/VisualizationTools.html
        - text: Evaluation of Dataset and Marker Gene Alignment
          href: articles/DatasetMarkerGeneAlignment.html
        - text: Detection and Analysis of Annotation Anomalies
          href: articles/AnnotationAnomalies.html
    - text: Reference
      href: reference/index.html
    - text: News
      href: news/index.html

reference:
  - title: Visualization of Cell Type Annotations
    contents:
      - boxplotPCA
      - calculateDiscriminantSpace
      - calculateSIRSpace
      - plotCellTypeMDS
      - plotCellTypePCA
  - title: Visualization of Marker Expressions
    contents:
      - plotGeneExpressionDimred
      - plotMarkerExpression
  - title: Visualization of QC and Annotation Scores
    contents:
      - histQCvsAnnotation
      - plotQCvsAnnotation
      - plotGeneSetScores
  - title: Evaluation of Dataset Alignment
    contents:
      - compareCCA
      - comparePCA
      - comparePCASubspace
      - plotPairwiseDistancesDensity
      - calculateWassersteinDistance
  - title: Evaluation of Marker Gene Alignment
    contents:
      - calculateHVGOverlap
      - calculateVarImpOverlap
  - title: Calculation of Statistical Measures to Compare Two Datasets
    contents:
      - calculateCramerPValue
      - calculateHotellingPValue
      - calculateNearestNeighborProbabilities
      - calculateAveragePairwiseCorrelation
      - regressPC
  - title: Anomaly Detection (Global and Cell Type-Specific)
    contents:
      - detectAnomaly
      - calculateCellSimilarityPCA
  - title: Calculation of Distances Between Specific Cells and Cell Populations
    contents:
      - calculateCellDistances
      - calculateCellDistancesSimilarity
  - title: Misc
    contents:
      - projectPCA
      - projectSIR
      - calculateCategorizationEntropy
  - title: Datasets
    contents:
      - reference_data
      - query_data
      - qc_data

right:
  - icon: fa-github
    href: https://github.com/ccb-hms/scDiagnostics