_pkgdown.yml

template:
  params:
    bootswatch: yeti

reference:
- title: "Start the Shiny APP"
- contents:
  - singleCellTK
- title: "Importing scRNA-seq Data"
- contents:
  - starts_with("import")
  - readSingleCellMatrix
- title: "Quality Control & Preprocessing"
- contents:
  - runCellQC
  - runDropletQC
  - runPerCellQC
  - reportDropletQC
  - reportCellQC
  - plotRunPerCellQCResults
- title: "Decontamination"
- contents:
  - runDecontX
  - plotDecontXResults
  - runSoupX
  - getSoupX<-
  - plotSoupXResults
- title: "Doublet/Empty Droplet Detection"
- contents:
  - runBarcodeRankDrops
  - runEmptyDrops
  - runBcds
  - runCxds
  - runCxdsBcdsHybrid
  - runScDblFinder
  - runDoubletFinder
  - runScrublet
  - plotBarcodeRankDropsResults
  - plotEmptyDropsResults
  - plotBcdsResults
  - plotCxdsResults
  - plotScdsHybridResults
  - plotScDblFinderResults
  - plotDoubletFinderResults
  - plotScrubletResults
- title: "Normalization"
- contents:
  - runNormalization
  - scaterlogNormCounts
  - scaterCPM
  - runSeuratNormalizeData
  - runSeuratScaleData
  - runSeuratSCTransform
  - computeZScore
  - trimCounts
- title: "Batch Effect Correction"
- contents:
  - runMNNCorrect
  - runComBatSeq
  - runBBKNN
  - runFastMNN
  - runLimmaBC
  - runHarmony
  - runSCANORAMA
  - runSCMerge
  - runSeuratIntegration
  - runZINBWaVE
  - plotBatchVariance
  - plotBatchCorrCompare
  - plotSCEBatchFeatureMean
- title: "Feature Selection"
- contents:
  - runFeatureSelection
  - runModelGeneVar
  - runSeuratFindHVG
  - getTopHVG
  - setTopHVG
  - plotTopHVG
- title: "Dimensionality Reduction & Embedding"
- contents:
  - runDimReduce
  - scaterPCA
  - runUMAP
  - runTSNE
  - runSeuratICA
  - runSeuratPCA
  - runSeuratUMAP
  - runSeuratTSNE
  - runQuickUMAP
  - runQuickTSNE
  - plotPCA
  - plotUMAP
  - plotTSNE
  - plotDimRed
  - plotSCEDimReduceColData
  - plotSCEDimReduceFeatures
- title: "Clustering"
- contents:
  - runScranSNN
  - runSeuratFindClusters
  - runKMeans
- title: "Differential Expression"
- contents:
  - runDEAnalysis
  - runWilcox
  - runMAST
  - runDESeq2
  - runLimmaDE
  - runANOVA
  - getDEGTopTable
  - plotDEGVolcano
  - plotDEGViolin
  - plotDEGRegression
  - plotDEGHeatmap
  - plotMASTThresholdGenes
- title: "Find Marker"
- contents:
  - runFindMarker
  - getFindMarkerTopTable
  - plotFindMarkerHeatmap
- title: "Differential Abundance"
- contents:
  - diffAbundanceFET
  - getDiffAbundanceResults
  - plotClusterAbundance
- title: "Cell Type Labeling"
- contents:
  - runSingleR
- title: "Enrichment & Pathway Analysis"
- contents:
  - getMSigDBTable
  - runEnrichR
  - getEnrichRResult<-
  - runGSVA
  - runVAM
  - getPathwayResultNames
  - plotPathway
- title: "Trajectory Analysis"
- contents:
  - starts_with("runTSCAN")
  - starts_with("plotTSCAN")
  - getTSCANResults
- title: "Seurat Curated Workflow"
- contents:
  - starts_with("runSeurat")
  - computeHeatmap
  - getSeuratVariableFeatures
- title: "Scanpy Curated Workflow"
- contents:
  - starts_with("runScanpy")
- title: "Visualization"
- contents:
  - starts_with("plot")
- title: "Report Generation"
- contents:
  - starts_with("report")
- title: "Exporting Results"
- contents:
  - starts_with("export")
- title: "Datasets"
- contents:
  - mouseBrainSubsetSCE
  - sceBatches
  - MitoGenes
  - msigdb_table
  - sce
  - SEG
- title: "Other Data Processing"
- contents:
  - starts_with("expData")
  - expDataNames
  - expDeleteDataTag
  - expSetDataTag
  - expTaggedData
  - calcEffectSizes
  - combineSCE
  - convertSCEToSeurat
  - convertSeuratToSCE
  - constructSCE
  - dedupRowNames
  - detectCellOutlier
  - discreteColorPalette
  - distinctColors
  - downSampleCells
  - downSampleDepth
  - featureIndex
  - retrieveSCEIndex
  - sampleSummaryStats
  - getSampleSummaryStatsTable
  - setSampleSummaryStatsTable<-
  - listSampleSummaryStatsTables
  - sctkListGeneSetCollections
  - getGenesetNamesFromCollection
  - setSCTKDisplayRow
  - subsetSCECols
  - subsetSCERows
  - generateHTANMeta
  - generateMeta
  - generateSimulatedData
  - getBiomarker
  - getSceParams
  - iterateSimulations
  - mergeSCEColData
  - qcInputProcess
  - setRowNames
  - subDiffEx
  - summarizeSCE
- title: "Python Environment Setting"
- contents:
  - sctkPythonInstallConda
  - selectSCTKConda
  - sctkPythonInstallVirtualEnv
  - selectSCTKVirtualEnvironment
navbar:
  title: "singleCellTK"
  left:
    - icon: fas fa-home fa-lg
      href: https://www.camplab.net/sctk
    - text: "Installation"
      href: articles/installation.html
    - text: "Tutorials"
      menu:
      - text: "Importing and QC - PBMC3K"
        href: articles/01_import_and_qc_tutorial.html
      - text: "A La Carte Workflow - PBMC3K"
        href: articles/02_a_la_carte_workflow.html
      - text: "Seurat Curated Workflow - PBMC3K"
        href: articles/seurat_curated_workflow.html
      - text: "Celda Curated Workflow - PBMC3K"
        href: articles/celda_curated_workflow.html
      - text: "Scanpy Curated Workflow - PBMC3K"
        href: articles/scanpy_curated_workflow.html
    - text: "SCTK-QC"
      href: articles/cmd_qc.html
    - text: "Documentation"
      menu:
        - text: "Data"
          menu:
            - text: "Import Data"
              href: articles/import_data.html
            - text: "Import Gene Sets"
              href: articles/import_genesets.html
            - text: "Annotation"
              href: articles/import_annotation.html
            - text: "Export Data"
              href: articles/export_data.html
            - text: "Delete Data"
              href: articles/delete_data.html
        - text: "QC & Filtering"
          menu:
            - text: "Droplet QC (R console)"
              href: articles/cnsl_dropletqc.html
            - text: "Cell QC (R console)"
              href: articles/cnsl_cellqc.html
            - text: "Cell QC (Shiny UI)"
              href: articles/ui_qc.html
            - text: "Filtering"
              href: articles/filtering.html
        - text: "Normalization & Batch Correction"
          menu:
          - text: "Normalization"
            href: articles/normalization.html
          - text: "Batch Correction"
            href: articles/batch_correction.html
        - text: "Feature Selection & Dimensionality Reduction"
          menu:
          - text: "Feature Selection"
            href: articles/feature_selection.html
          - text: "Dimensionality Reduction"
            href: articles/dimensionality_reduction.html
          - text: "2D Embedding"
            href: articles/2d_embedding.html
        - text: "Clustering"
          href: articles/clustering.html
        - text: "Differential Expression & Cell Type Labeling"
          menu:
            - text: "Differential Expression"
              href: articles/differential_expression.html
            - text: "Find Marker"
              href: articles/find_marker.html
            - text: "Cell Type Labeling"
              href: articles/cell_type_labeling.html
        - text: "Pathway & Enrichment Analysis"
          menu:
            - text: "EnrichR"
              href: articles/enrichR.html
            - text: "Pathway Analysis"
              href: articles/pathwayAnalysis.html
        - text: "Trajectory Analysis"
          menu:
            - text: "TSCAN"
              href: articles/trajectoryAnalysis.html
        - text: "Curated Workflows"
          menu:
            - text: "Seurat"
              href: articles/seurat_curated_workflow.html
            - text: "Celda"
              href: articles/celda_curated_workflow.html
        - text: "Visualization"
          menu:
          - text: "General Visualization"
            href: articles/visualization.html
          - text: "Generic Heatmap"
            href: articles/heatmap.html
    - text: "Reference"
      href: reference/index.html
    - text: "NEWS"
      href: news/index.html
  right:
    - icon: fab fa-github fa-lg
      href: https://github.com/compbiomed/singleCellTK
    - icon: fab fa-twitter fa-lg
      href: https://twitter.com/camplab1