template:
  params:
    bootswatch: yeti

reference:
  - title: Shiny App
    contents:
    - singleCellTK
  - title: Data Summary and Filtering
    contents:
    - filterSCData
    - summarizeTable
    - convertGeneIDs
  - title: Dimensionality Reduction and Clustering
    contents:
    - getPCA
    - getTSNE
    - getBiomarker
    - getClusterInputData
    - plotBiomarker
    - plotPCA
    - plotTSNE
  - title: Batch Correction
    contents:
    - plotBatchVariance
    - ComBatSCE
  - title: Differential Expression
    contents:
    - scDiffEx
    - scDiffExANOVA
    - scDiffExDESeq2
    - scDiffExlimma
    - plotDiffEx
    - MAST
    - MASTregression
    - MASTviolin
    - thresholdGenes
  - title: Pathway Activity Analysis
    contents:
    - gsvaPlot
    - gsvaSCE
  - title: Sample Size
    contents:
    - calcEffectSizes
    - DownsampleCells
    - DownsampleDepth
    - generateSimulatedData
    - iterateSimulations
    - subDiffEx
    - subDiffExANOVA
    - subDiffExttest
  - title: Data
    contents:
    - mouseBrainSubsetSCE
  - title: SCtkExperiment
    contents:
    - createSCE
    - starts_with("SCtkExperiment")
    - starts_with("pcaVariances")
  - title: Alignment
    contents:
    - alignSingleCellData
    - parseRsubreadLogs

navbar:
  title: "singleCellTK"
  left:
    - text: "Introduction to singleCellTK"
      href: articles/v01-Introduction_to_singleCellTK.html
    - text: "Interactive Shiny Analysis"
      menu:
        - text: "1: Upload"
          href: articles/v03-tab01_Upload.html
        - text: "2: Data Summary and Filtering"
          href: articles/v04-tab02_Data-Summary-and-Filtering.html
        - text: "3: Visualization and Clustering"
          href: articles/v05-tab03_Visualization-and-Clustering.html
        - text: "4: Batch Correction"
          href: articles/v06-tab04_Batch-Correction.html
        - text: "5: Differential Expression"
          href: articles/v07-tab05_Differential-Expression.html
        - text: "6: Pathway Activity Analysis"
          href: articles/v08-tab06_Pathway-Activity-Analysis.html
        - text: "7: Sample Size"
          href: articles/v09-tab07_Sample-Size.html
    - text: "Command Line Analysis"
      menu:
        - text: "Processing and Visualizing Data"
          href: articles/v02-Processing_and_Visualizing_Data_in_the_SingleCellTK.html
        - text: "Aligning and Quantifying scRNA-Seq Data"
          href: articles/v10-Aligning_and_Quantifying_scRNA-Seq_Data.html
    - text: "Reference"
      href: reference/index.html
  right:
    - icon: fa-github
      href: https://github.com/compbiomed/singleCellTK