.Rbuildignore
.github/workflows/main.yml
.gitignore
CONDUCT.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/ALPACA.R
R/BLOBFISH.R
R/COBRA.R
R/CONDOR.R
R/CRANE.R
R/DRAGON.R
R/EGRET.R
R/LIONESS.R
R/MONSTER.R
R/OTTER.R
R/PANDA.R
R/PUMA.R
R/SAMBAR.R
R/SPIDER.R
R/TIGER.R
R/YARN.R
R/createDiffPandaStyle.R
R/createPandaStyle.R
R/pandaDiffEdges.R
R/pandaToAlpaca.R
R/pandaToCondorObject.R
R/sourcePPI.R
R/visDiffPandaInCytoscape.R
R/visPandaInCytoscape.R
R/zzz.R
README.md
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docs/reference/filterLowGenes.html
docs/reference/filterMissingGenes.html
docs/reference/filterSamples.html
docs/reference/genes.html
docs/reference/index.html
docs/reference/isElist.html
docs/reference/jutterDegree.html
docs/reference/lioness.html
docs/reference/lioness.py.html
docs/reference/lionessPy.html
docs/reference/monster.bereFull.html
docs/reference/monster.calculate.tm.p.values.html
docs/reference/monster.checkDataType.html
docs/reference/monster.dTFIPlot-1.png
docs/reference/monster.dTFIPlot.html
docs/reference/monster.hcl.heatmap.plot-1.png
docs/reference/monster.hcl.heatmap.plot.html
docs/reference/monster.html
docs/reference/monster.monsterNI.html
docs/reference/monster.plot.monsterAnalysis-1.png
docs/reference/monster.plot.monsterAnalysis.html
docs/reference/monster.print.monsterAnalysis.html
docs/reference/monster.transformation.matrix.html
docs/reference/monster.transitionNetworkPlot-1.png
docs/reference/monster.transitionNetworkPlot-2.png
docs/reference/monster.transitionNetworkPlot.html
docs/reference/monster.transitionPCAPlot-1.png
docs/reference/monster.transitionPCAPlot.html
docs/reference/monsterBereFull.html
docs/reference/monsterCalculateTmPvalues.html
docs/reference/monsterCheckDataType.html
docs/reference/monsterGetTm.html
docs/reference/monsterHclHeatmapPlot-1.png
docs/reference/monsterHclHeatmapPlot.html
docs/reference/monsterMonsterNI.html
docs/reference/monsterPlotMonsterAnalysis-1.png
docs/reference/monsterPlotMonsterAnalysis.html
docs/reference/monsterPrintMonsterAnalysis.html
docs/reference/monsterRes.html
docs/reference/monsterTransformationMatrix.html
docs/reference/monsterTransitionPCAPlot-1.png
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docs/reference/monsterdTFIPlot-1.png
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docs/reference/monstertransitionNetworkPlot-1.png
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docs/reference/monstertransitionNetworkPlot.html
docs/reference/mut.ucec.html
docs/reference/normalizeTissueAware.html
docs/reference/otter.html
docs/reference/panda.diff.edges.html
docs/reference/panda.py.html
docs/reference/panda.to.alpaca.html
docs/reference/panda.to.condor.object-1.png
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docs/reference/panda.to.condor.object.html
docs/reference/pandaDiffEdges.html
docs/reference/pandaPy.html
docs/reference/pandaToAlpaca.html
docs/reference/pandaToCondorObject-1.png
docs/reference/pandaToCondorObject.html
docs/reference/plotCMDS.html
docs/reference/plotDensity.html
docs/reference/plotHeatmap.html
docs/reference/prior.pp.html
docs/reference/priorPp.html
docs/reference/puma.html
docs/reference/qsmooth.html
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docs/reference/runEgret.html
docs/reference/sambar.convertgmt.html
docs/reference/sambar.corgenelength.html
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docs/reference/sambar.html
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docs/reference/sambarCorgenelength.html
docs/reference/sambarDesparsify.html
docs/reference/small1976.html
docs/reference/source.PPI.html
docs/reference/sourcePPI.html
docs/reference/spider.html
docs/reference/tiger.html
docs/reference/vis.diff.panda.in.cytoscape.html
docs/reference/vis.panda.in.cytoscape.html
docs/reference/visDiffPandaInCytoscape.html
docs/reference/visPandaInCytoscape.html
docs/reference/yeast.html
docs/search.json
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inst/CITATION
inst/extdata/Example_2comm.txt
inst/extdata/chip_matched.txt
inst/extdata/chip_medium.txt
inst/extdata/chip_reduced.txt
inst/extdata/expr10_matched.txt
inst/extdata/expr10_reduced.txt
inst/extdata/expr4_matched.txt
inst/extdata/h.all.v6.1.symbols.gmt
inst/extdata/lioness.py
inst/extdata/panda.py
inst/extdata/ppi_matched.txt
inst/extdata/ppi_reduced.txt
inst/extdata/toy_eQTL.txt
inst/extdata/toy_expr.txt
inst/extdata/toy_genotype.vcf
inst/extdata/toy_map.txt
inst/extdata/toy_motif_prior.txt
inst/extdata/toy_ppi_prior.txt
inst/extdata/toy_qbic.txt
inst/script/instDataReadme.md
man/BuildSubnetwork.Rd
man/CalculatePValues.Rd
man/FindConnectionsForAllHopCounts.Rd
man/FindSignificantEdgesForHop.Rd
man/GenerateNullPANDADistribution.Rd
man/PlotNetwork.Rd
man/RunBLOBFISH.Rd
man/SignificantBreadthFirstSearch.Rd
man/TIGER_expr.Rd
man/TIGER_prior.Rd
man/adj2el.Rd
man/adj2regulon.Rd
man/adjMatToElist.Rd
man/alpaca.Rd
man/alpacaCommunityStructureRotation.Rd
man/alpacaComputeDWBMmatmScale.Rd
man/alpacaComputeDifferentialScoreFromDWBM.Rd
man/alpacaComputeWBMmat.Rd
man/alpacaCrane.Rd
man/alpacaDeltaZAnalysis.Rd
man/alpacaDeltaZAnalysisLouvain.Rd
man/alpacaExtractTopGenes.Rd
man/alpacaGOtabtogenes.Rd
man/alpacaGenLouvain.Rd
man/alpacaGetMember.Rd
man/alpacaGoToGenes.Rd
man/alpacaListToGo.Rd
man/alpacaMetaNetwork.Rd
man/alpacaNodeToGene.Rd
man/alpacaObjectToDfList.Rd
man/alpacaRotationAnalysis.Rd
man/alpacaRotationAnalysisLouvain.Rd
man/alpacaSimulateNetwork.Rd
man/alpacaTestNodeRank.Rd
man/alpacaTidyConfig.Rd
man/alpacaTopEnsembltoTopSym.Rd
man/alpacaWBMlouvain.Rd
man/annotateFromBiomart.Rd
man/bladder.Rd
man/checkMisAnnotation.Rd
man/checkTissuesToMerge.Rd
man/cobra.Rd
man/condorCluster.Rd
man/condorCoreEnrich.Rd
man/condorCreateObject.Rd
man/condorMatrixModularity.Rd
man/condorModularityMax.Rd
man/condorPlotCommunities.Rd
man/condorPlotHeatmap.Rd
man/condorQscore.Rd
man/condorRun.Rd
man/craneBipartite.Rd
man/craneUnipartite.Rd
man/createCondorObject.Rd
man/createPandaStyle.Rd
man/degreeAdjust.Rd
man/domonster.Rd
man/downloadGTEx.Rd
man/dragon.Rd
man/el2adj.Rd
man/el2regulon.Rd
man/elistAddTags.Rd
man/elistIsEdgeOrderEqual.Rd
man/elistRemoveTags.Rd
man/elistSort.Rd
man/elistToAdjMat.Rd
man/exon.size.Rd
man/extractMatrix.Rd
man/filterGenes.Rd
man/filterLowGenes.Rd
man/filterMissingGenes.Rd
man/filterSamples.Rd
man/genes.Rd
man/isElist.Rd
man/jutterDegree.Rd
man/lioness.Rd
man/lionessPy.Rd
man/monster.Rd
man/monsterBereFull.Rd
man/monsterCalculateTmPValues.Rd
man/monsterCheckDataType.Rd
man/monsterGetTm.Rd
man/monsterHclHeatmapPlot.Rd
man/monsterMonsterNI.Rd
man/monsterPlotMonsterAnalysis.Rd
man/monsterPrintMonsterAnalysis.Rd
man/monsterRes.Rd
man/monsterTransformationMatrix.Rd
man/monsterTransitionNetworkPlot.Rd
man/monsterTransitionPCAPlot.Rd
man/monsterdTFIPlot.Rd
man/mut.ucec.Rd
man/normalizeTissueAware.Rd
man/otter.Rd
man/pandaDiffEdges.Rd
man/pandaPy.Rd
man/pandaToAlpaca.Rd
man/pandaToCondorObject.Rd
man/plotCMDS.Rd
man/plotDensity.Rd
man/plotHeatmap.Rd
man/priorPp.Rd
man/puma.Rd
man/qsmooth.Rd
man/qstats.Rd
man/runEgret.Rd
man/sambar.Rd
man/sambarConvertgmt.Rd
man/sambarCorgenelength.Rd
man/sambarDesparsify.Rd
man/skin.Rd
man/small1976.Rd
man/sourcePPI.Rd
man/spider.Rd
man/tiger.Rd
man/visPandaInCytoscape.Rd
man/yeast.Rd
tests/testthat.R
tests/testthat/test-alpaca.R
tests/testthat/test-blobfish.R
tests/testthat/test-condor.R
tests/testthat/test-dragon.R
tests/testthat/test-egret.R
tests/testthat/test-lioness.R
tests/testthat/test-monster.R
tests/testthat/test-otter.R
tests/testthat/test-panda.R
tests/testthat/test-pandadiffedges.R
tests/testthat/test-pandatoalpaca.R
tests/testthat/test-pandatocondorobject.R
tests/testthat/test-sambar.R
tests/testthat/test-source.PPI.R
vignettes/.gitignore
vignettes/ALPACA.Rmd
vignettes/ApplicationinGTExData.Rmd
vignettes/ApplicationwithTBdataset.Rmd
vignettes/CONDOR.Rmd
vignettes/EGRET_toy_example.Rmd
vignettes/LionessApplicationinGTExData.Rmd
vignettes/MONSTER.Rmd
vignettes/SAMBAR.Rmd
vignettes/TutorialOTTER.Rmd
vignettes/pandaR.Rmd
vignettes/pandaRApplicationinGTExData.Rmd
vignettes/toy_genotype.vcf
vignettes/yarn.Rmd