_pkgdown.yml

template:
  bootstrap: 5
  bslib:
    info: "#E6F2FD"
    base_font:
      google: {family: "Atkinson Hyperlegible", wght: [300, 400, 700], ital: [0, 1]}
    headings-color: "#206B72"
    link-color: "#216B73"
    link-color-dark: "#cef4f9"
    link-decoration: underline dotted

reference:
- title: "Read Data"
- contents:
  - starts_with("create")
  - readLiger
  - read10X
  - as.ligerDataset
  - as.liger
- title: "Example Data"
- contents:
  - importBMMC
  - importCGE
  - importPBMC
  - pbmc
  - pbmcPlot
  - bmmc
- title: "Preprocessing"
- contents:
  - runGeneralQC
  - runDoubletFinder
  - removeMissing
  - normalize
  - selectGenes
  - scaleNotCenter
  - reverseMethData
  - downsample
  - selectGenesVST
- title: "Integration"
- subtitle: "Perform iNMF and Variants"
- contents:
  - runIntegration
  - runINMF
  - runOnlineINMF
  - runUINMF
  - runCINMF
- subtitle: "Post-Factorization Alignment"
- contents:
  - quantileNorm
- subtitle: "Evaluation"
- contents:
  - calcAlignment
  - calcAgreement
  - calcDatasetSpecificity
- subtitle: "Optimization with New Parameter"
- contents:
  - optimizeNewData
  - optimizeNewK
  - optimizeNewLambda
  - optimizeSubset
- title: "Downstream Analysis"
- subtitle: "Dimensionality Reduction"
- contents:
  - runUMAP
  - runTSNE
- subtitle: "Clustering"
- contents:
  - runCluster
  - mapCellMeta
  - calcARI
  - calcPurity
- subtitle: "Differential Expression"
- contents:
  - runMarkerDEG
  - runPairwiseDEG
  - runWilcoxon
  - getFactorMarkers
- subtitle: "GO and GSEA"
- contents:
  - runGOEnrich
  - runGSEA
- subtitle: "ATAC Specific Analysis"
- contents:
  - imputeKNN
  - linkGenesAndPeaks
  - exportInteractTrack
- title: "Visualization"
- contents:
  - starts_with("plot")
  - makeRiverplot
  - starts_with(".gg")
  - starts_with(".plot")
  - .complexHeatmapDotPlot
- title: "Object Class"
- contents:
  - ends_with("class")
  - sub-liger
  - sub-sub-liger
  - sub-ligerDataset
  - rawPeak
  - coordinate
  - retrieveCellFeature
  - subsetLiger
  - subsetLigerDataset
  - convertOldLiger
  - ligerToSeurat
  - is.newLiger
  - modalOf
  - isH5Liger
  - restoreH5Liger
  - closeAllH5
- title: "Misc"
- contents:
  - H5Apply
  - commandDiff
  - makeFeatureMatrix
  - mergeH5
  - mergeSparseAll
  - writeH5
- title: "Deprecated"
- contents:
  - ends_with("deprecated")
  - readSubset
  - quantileAlignSNF
  - getProportionMito
navbar:
  title: "rliger"
  left:
    - text: "Installation"
      href: articles/installation.html
    - text: "Tutorials"
      menu:
        - text: "Integrating multiple scRNAseq data"
          href: articles/Integrating_multi_scRNA_data.html
        - text: "Integrating scRNA and scATAC data"
          href: articles/Integrating_scRNA_and_scATAC_data.html
        - text: "Online iNMF with HDF5 based data"
          href: articles/online_iNMF_tutorial.html
        - text: "Integration using unshared features"
          href: articles/UINMF_vignette.html
        - text: "Cross-species Analysis with UINMF"
          href: articles/cross_species_vig.html
        - text: "UINMF with STARmap spatial and transcriptomic"
          href: articles/STARmap_dropviz_vig.html
        - text: "UINMF with SNAREseq scATAC and scRNA"
          href: articles/SNAREseq_walkthrough.html
        - text: "Integrating scRNAseq and DNA methylation"
          href: articles/rna_methylation.html
    - text: "Usage"
      menu:
        - text: "Import data"
          href: articles/import_data.html
        - text: "Introduction to a liger object"
          href: articles/liger_object.html
        - text: "Interoperate with Seurat"
          href: articles/liger_with_seurat.html
    - text: "Reference"
      href: reference/index.html
    - text: "NEWS"
      href: news/index.html
  right:
    - text: Welch Lab
      href: https://welch-lab.github.io/
    - icon: fab fa-github fa-lg
      href: https://github.com/welch-lab/liger
    - icon: fab fa-twitter fa-lg
      href: https://twitter.com/LabWelch