template:
  params:
    bootswatch: yeti

reference:
- title: "Importing scRNA-seq data"
- contents:
  - starts_with("import")
  - readSingleCellMatrix
- title: "Quality Control & Preprocessing"
- contents:
  - runCellQC
  - runDropletQC
- title: "Decontamination"
- contents:
  - runDecontX
- title: "Doublet/Empty Droplet Detection"
- contents:
  - runBarcodeRankDrops
  - runEmptyDrops
  - runBcds
  - runCxds
  - runCxdsBcdsHybrid
  - runScDblFinder
  - runDoubletFinder
  - runScrublet
- title: "Normalization"
- contents:
  - runNormalization
  - scaterlogNormCounts
  - scaterCPM
  - seuratNormalizeData
  - seuratScaleData
  - computeZScore
  - trimCounts
- title: "Batch Effect Correction"
- contents:
  - runComBatSeq
  - runBBKNN
  - runFastMNN
  - runLimmaBC
  - runMNNCorrect
  - runSCANORAMA
  - runSCMerge
  - seuratIntegration
  - runZINBWaVE
  - plotBatchVariance
- title: "Feature Selection"
- contents:
  - scranModelGeneVar
  - seuratFindHVG
  - getTopHVG
  - seuratPlotHVG
- title: "Dimensionality Reduction"
- contents:
  - scaterPCA
  - getUMAP
  - getTSNE
  - seuratICA
  - seuratPCA
  - seuratRunUMAP
  - seuratRunTSNE
  - plotSCEDimReduceColData
  - plotSCEDimReduceFeatures
- title: "Clustering"
- contents:
  - runScranSNN
  - seuratFindClusters
  - runKMeans
- title: "Differential Expression"
- contents:
  - runDEAnalysis
  - runWilcox
  - runMAST
  - runDESeq2
  - runLimmaDE
  - runANOVA
  - plotDEGViolin
  - plotDEGRegression
  - plotDEGHeatmap
  - plotMASTThresholdGenes
- title: "Find Marker"
- contents:
  - findMarkerDiffExp
  - plotMarkerDiffExp
- title: "Visualization"
- contents:
  - starts_with("plot")
- title: "Exporting Results"
- contents:
  - starts_with("export")
- title: "Other Data processing"
- contents:
  - combineSCE
  - convertSCEToSeurat
  - convertSeuratToSCE
  - subsetSCECols
  - subsetSCERows
  - dedupRowNames
navbar:
  title: "singleCellTK"
  left:
    - text: "General Workflow"
      href: articles/articles/introduction_to_SCTK.html
    - text: "Shell Command Line Analysis"
      menu:
        - text: "Import data into SCTK"
          href: articles/articles/cmd_import_scRNAseq_data_as_SCE.html
        - text: "Quality Control"
          href: articles/articles/cmd_qc.html
    - text: "R Console Analysis"
      menu:
        - text: "Import data into SCTK"
          href: articles/articles/cnsl_import_scRNAseq_data_as_SCE.html
        - text: "Quality Control"
          href: articles/articles/cnsl_qc.html
        - text: "Normalization"
          href: articles/articles/cnsl_normalization.html
        - text: "Batch Correction"
          href: articles/articles/cnsl_batch_correction.html
        - text: "Feature Selection"
          href: articles/articles/cnsl_feature_selection.html
        - text: "Dimensionality Reduction"
          href: articles/articles/cnsl_dimensionality_reduction.html
        - text: "Clustering"
          href: articles/articles/cnsl_clustering.html
        - text: "Differential Expression"
          menu:
            - text: "Differential Expression"
              href: articles/articles/cnsl_differential_expression.html
            - text: "Find Marker via DE"
              href: articles/articles/cnsl_find_marker.html
        - text: "Enrichment Analysis"
          menu:
            - text: "GSVA"
              href: articles/articles/cnsl_gsva.html
            - text: "EnrichR"
              href: articles/articles/cnsl_enrichR.html
        - text: "Visualization"
          menu:
            - text: "General Visualization"
              href: articles/articles/cnsl_visualization.html
            - text: "Heatmap Visualization"
              href: articles/articles/cnsl_heatmap.html
        - text: "Curated Workflows"
          menu:
            - text: "Seurat"
              href: articles/articles/cnsl_seurat_curated_workflow.html
            - text: "Celda"
              href: articles/articles/cnsl_celda_curated_workflow.html
    - text: "Shiny UI Analysis"
      menu:
        - text: "Data"
          menu:
            - text: "Import Data"
              href: articles/articles/ui_import_data.html
            - text: "Import Gene Sets"
              href: articles/articles/ui_import_genesets.html
            - text: "Annotation"
              href: articles/articles/ui_import_annotation.html
            - text: "Export Data"
              href: articles/articles/ui_export_data.html
            - text: "Delete Data"
              href: articles/articles/ui_delete_data.html
        - text: "QC & Filtering"
          menu:
            - text: "Quality Control"
              href: articles/articles/ui_qc.html
            - text: "Filtering"
              href: articles/articles/ui_filtering.html
        - text: "Normalization & Batch Correction"
          menu:
          - text: "Normalization"
            href: articles/articles/ui_normalization.html
          - text: "Batch Correction"
            href: articles/articles/ui_batch_correction.html
        - text: "Feature Selection & Dimensionality Reduction"
          menu:
          - text: "Feature Selection"
            href: articles/articles/ui_feature_selection.html
          - text: "Dimensionality Reduction"
            href: articles/articles/ui_dimemsionality_reduction.html
        - text: "Clustering"
          href: articles/articles/ui_clustering.html
        - text: "Differential Expression & Cell Type Labeling"
          menu:
            - text: "Differential Expression"
              href: articles/articles/ui_differential_expression.html
            - text: "Find Marker"
              href: articles/articles/ui_find_marker.html
        - text: "Curated Workflows"
          menu:
            - text: "Seurat"
              href: articles/articles/ui_seurat_curated_workflow.html
        - text: "Visualization"
          menu:
          - text: "cellViewer"
            href: articles/articles/ui_cellViewer.html
          - text: "Generic Heatmap"
            href: articles/articles/ui_heatmap.html
    - text: "Reference"
      href: reference/index.html
  right:
    - icon: fa-github
      href: https://github.com/compbiomed/singleCellTK