Files in netZoo/netZooR
Unified methods for the inference and analysis of gene regulatory networks

.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
_pkgdown.yml
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data/exon.size.RData
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data/monsterRes.RData
data/mut.ucec.RData
data/small1976.rda
data/yeast.RData
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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
docs/reference/monsterTransitionPCAPlot.html
docs/reference/monsterdTFIPlot-1.png
docs/reference/monsterdTFIPlot.html
docs/reference/monstertransitionNetworkPlot-1.png
docs/reference/monstertransitionNetworkPlot-2.png
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
docs/reference/qstats.html
docs/reference/runEgret.html
docs/reference/sambar.convertgmt.html
docs/reference/sambar.corgenelength.html
docs/reference/sambar.desparsify.html
docs/reference/sambar.html
docs/reference/sambarConvertgmt.html
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
docs/sitemap.xml
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
netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.