_pkgdown.yml

template:
  bootstrap: 5
destination: docs
reference:
- title: Main functions
  desc:  main functions to run each algorithm
  contents:
  - pandaPy
  - createCondorObject
  - lioness
  - alpaca
  - sambar
  - monster
  - otter
  - cobra
  - puma
  - spider
  - tiger
  - runEgret
  - dragon
  - craneBipartite

- title: PANDA
  desc: All functions of PANDA
  contents:
  - pandaPy
  - pandaToCondorObject
  - pandaToAlpaca
  - pandaDiffEdges
  - visPandaInCytoscape
  - createPandaStyle

- title: CONDOR
  desc: All functions of CONDOR
  contents:
  - createCondorObject
  - starts_with("condor")


- title: LIONESS
  desc: All functions of LIONESS
  contents:
  - lionessPy
  - lioness

- title: ALPACA
  desc: All functions of ALPACA
  contents:
  - starts_with("alpaca")

- title: SAMBAR
  desc: All functions of SAMBAR
  contents:
  - starts_with("sambar")

- title: MONSTER
  desc: All functions of MONSTER
  contents:
  - starts_with("monster")

- title: OTTER
  desc: OTTER functions
  contents:
  - otter

- title : TIGER
  desc: TIGER functions
  contents:
  - tiger
  - TIGER_expr
  - TIGER_prior
  - adj2regulon
  - priorPp

- title : COBRA
  desc: COBRA functions
  contents:
  - cobra

- title: CRANE
  desc: CRANE functions
  contents:
  - craneBipartite
  - craneUnipartite
  - elistToAdjMat
  - elistSort
  - elistRemoveTags
  - elistSort
  - isElist
  - adjMatToElist
  - el2adj
  - el2regulon
  - elistIsEdgeOrderEqual
  - elistAddTags
  - adj2el
  - jutterDegree

- title: DRAGON
  desc: DRAGON functions
  contents:
  - dragon

- title: SPIDER
  desc: SPIDER functions
  contents:
  - spider
  - degreeAdjust

- title: PUMA
  desc: PUMA functions
  contents:
  - puma

- title: EGRET
  desc: EGRET functions
  contents:
  - runEgret

- title: BLOBFISH
  desc: BLOBFISH functions
  contents:
  - RunBLOBFISH
  - GenerateNullPANDADistribution
  - BuildSubnetwork
  - CalculatePValues
  - FindSignificantEdgesForHop
  - SignificantBreadthFirstSearch
  - FindConnectionsForAllHopCounts
  - PlotNetwork

- title: YARN
  desc: YARN functions
  contents:
  - checkMisAnnotation
  - checkTissuesToMerge
  - filterGenes
  - filterLowGenes
  - normalizeTissueAware
  - annotateFromBiomart
  - downloadGTEx
  - extractMatrix
  - filterMissingGenes
  - filterSamples
  - plotCMDS
  - plotDensity
  - plotHeatmap
  - qsmooth
  - qstats

- title: Plotting functions
  desc: function to plot the networks and community structures.
  contents:
  - createPandaStyle
  - condorPlotCommunities
  - condorPlotHeatmap

- title: Helper functions
  desc: miscellaneous function
  contents:
  - sourcePPI
  - pandaToCondorObject
  - pandaToAlpaca

- title: Data
  desc: Input example data files
  contents:
  - yeast
  - small1976
  - mut.ucec
  - exon.size
  - genes
  - Bladder_data
  - Skin_data