_pkgdown.yml

authors:
  Nicholas Mikolajewicz:
    href: https://scholar.google.ca/scholar?hl=en&as_sdt=0%2C5&q=mikolajewicz+nicholas&oq=
url: https://github.com/NMikolajewicz/
title: scMiko
template:
  params:
    bootswatch: flatly

development:
  mode: unreleased

navbar:
  title: "scMiko"
  left:
    - text: "Getting Started"
      menu:
        - text: Computational Resources
        - text: "scMiko Package"
          href: articles/install.html
        - text: "scPipeline Reports"
          href: articles/scPipeline_getting_started.html
    - text: "Vignettes"
      menu:
        - text: scMiko Vignettes
        - text: "Differential-expression using CDI"
          href: articles/DEG.html
        - text: "Selecting cluster resolution using specificity criterion"
          href: articles/Cluster_Optimization.html
        - text: "Cell-type marker catalog"
          href: articles/Marker_Catalog.html
        - text: "Marker-based cell-type annotation using Miko Scoring"
          href: articles/Cell_Annotation.html
        - text: "Gene program discovery using SSN analysis"
          href: articles/Module_Detection.html
        - text: -------
        - text: scPipeline Dashboard Reports
        - text: "Overview of modules"
          href: articles/scPipeline_module_overview.html
    - text: "Reference"
      href: reference/index.html
  right:
    - icon: fa-github
      href: https://github.com/NMikolajewicz/scMiko



reference:

- title: "Filters and QC"
- contents:
  - filterSeurat
  - clusterFilter
  - cleanCluster
  - cleanFilterGenes
  - findArtifactGenes
  - getExpressedGenes
  - getExpressingCells
  - getMitoContent
  - QC.scatterPlot
  - QC.violinPlot

- title: "Dimensional Reduction"
- contents:
  - pcaElbow
  - projectReduction
  - propVarPCA
  - getReductionGenes
  - runRPCA

- title: "Clustering"
- contents:
  - setResolution
  - multiCluster
  - multiSpecificity
  - multiSilhouette

- title: "Cell-Type Annotation"
  desc: "Module detection"
- contents:
  - mikoScore
  - nullScore
  - sigScore

- title: "Gene Set Functions"
- contents:
  - AddSModuleScore
  - aggGroupExpression
  - avgGroupExpression
  - coherentFraction
  - consolidateNMF
  - getJaccard
  - id2geneset
  - id2term
  - jaccardSimilarityMatrix
  - optimalBinSize
  - runAUC
  - runMS
  - has_concept("enrichment")
  - baderPathways
  - getAnnotationPathways
  - runGSEA
  - runHG
  - searchAnnotations
  - signatureCoherence
  - summarizeHG
  - term2id
  - upset.Plot


- title: "Expression Functions"
- contents:
  - findCDIMarkers
  - findConservedCDIMarkers
  - findCorMarkers
  - findGiniMarkers
  - getDEG
  - getExpressionMatrix
  - miko_volcano
  - parCor
  - pseudotimeRF

- title: "Variance Decomposition"
  desc: "Variance decomposition analyses"
- contents:
  - matches("vd")

- title: "Scale-Free Shared Nearest Neighbor Network Analysis (SSN)"
  desc: "SSN Module detection"
- contents:
  - SSNConnectivity
  - SSNResolution
  - matches("SSN")
  - findNetworkFeatures
  - getModuleGenes
  - pruneSSN
  - runSSN
  - scaleFreeNet
  - SSNExpression
  - summarizeModules

- title: "Independent Component Analysis"
  desc: "ICA Module detection"
- contents:
  - getICAGenes
  - runICA

- title: "Non-Negative Matrix Factorization"
  desc: "NMF Module detection"
- contents:
  - getNMFGenes
  - runNMF

# - title: "WGCNA"
#   desc: "WGCNA Module detection"
# - contents:
#   - getModulePreservation
#   - getSoftThreshold
#   - getSoftThreshold2
#   - optimalDS
#   - runWGCNA
#   - scaleTOM
#   - wgcna2graphDF


- title: "Differential Abundance Analysis"
- contents:
  - da_DEG
  - da_Run


- title: "Visualization"
- contents:
  - cluster.UMAP
  - expression.Plot
  - exprUMAP
  - featureGradient
  - geneRepCurve
  - geom_split_violin
  - getUMAP
  - miko_heatmap
  - scale_color_miko
  - scale_fill_miko
  - scExpression.UMAP
  - theme_miko
  - variableGenes.Plot
  - highlightUMAP

- title: "Data"
- contents:
  - geneSets
  - LR.db

- title: "Miscellaneous Utilities"
- contents:
  - autoPointSize
  - balanceMatrixSize
  - categoricalColPal
  - citationCheck
  - clearGlobalEnv
  - col2rowname
  - dist2hclust
  - fixBarcodeLabel
  - getClusterCenters
  - getConnectivity
  - getDensity
  - getNodesEdges
  - getOrderedGroups
  - group2list
  - lintersect
  - longDF2namedList
  - miko_message
  - namedList2longDF
  - namedList2wideDF
  - orderedFactor
  - pseudoReplicates
  - qNorm
  - rescaleValues
  - rmvCSVprefix
  - scoreGBM
  - snip
  - sim2adj
  - sparse2dense
  - sparse2df
  - ulength
  - value2col
  - wideDF2namedList

- title: "Integration Functions"
- contents:
  - miko_integrate
  - runScanorama
  - runBBKNN

- title: "Seurat Functions"
- contents:
  - balanceSamples
  - downsampleSeurat
  - mergeSeuratList
  - neighborPurity
  - prepSeurat
  - prepSeurat2
  - recodeBarcode
  - rmDuplicateGenes
  - scNormScale
  - subsetDimRed
  - uniqueFeatures
  - updateDimNames
  - wnn_Components
  - wnn_Run

- title: "Gene Representation"
- contents:
  - checkGeneRep
  - detectSpecies
  - ens2sym.so
  - ensembl2sym
  - entrez2sym
  - firstup
  - inferSpecies
  - prepGeneList
  - speciesConvert
  - sym2ens
  - sym2entrez

- title: "Dashboard Utilities"
- contents:
  - addLogEntry
  - barcodeLabels
  - flex.asDT
  - flex.multiTabLogs
  - flex.multiTabPlot
  - flex.multiTabPlotly
  - flex.multiTabTables
  - getLoadPath
  - initiateLog
  - loadCellRanger
  - loadMat
  - loadMoffat
  - updateCentralLog

- title: "Save Functions"
- contents:
  - saveHTML
  - savePDF



# Run once to configure your package to use pkgdown
# usethis::use_pkgdown()

# Run to build the website
# pkgdown::build_site()
# pkgdown::build_site(lazy = T)