Files in farrellja/URD

URD

.gitignore

Analyses/QuickStart/URD-QuickStart-AxialMesoderm.Rmd Analyses/QuickStart/URD-QuickStart-AxialMesoderm.md

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Analyses/QuickStart/data/count.axial.txt.gz

Analyses/QuickStart/data/meta.axial.txt.gz

Analyses/SupplementaryAnalysis/SupplementaryAnalysis.pdf Analyses/SupplementaryAnalysis/URD-01-CreatingURDObject.Rmd Analyses/SupplementaryAnalysis/URD-02-CalculatingAndInspectingDiffusionMap.Rmd Analyses/SupplementaryAnalysis/URD-03-ClusteringAndDeterminingTips.Rmd Analyses/SupplementaryAnalysis/URD-04-BiasedRandomWalks.Rmd Analyses/SupplementaryAnalysis/URD-05-BuildTree.Rmd Analyses/SupplementaryAnalysis/URD-06-GeneExpressionCascades.Rmd Analyses/SupplementaryAnalysis/URD-07-Plotting.Rmd Analyses/SupplementaryAnalysis/URD-08-ComparingDiffusionMaps.Rmd Analyses/SupplementaryAnalysis/URD-09-BiasedRandomWalksComparison.Rmd Analyses/SupplementaryAnalysis/URD-10-ConnectModulesBetweenStages.Rmd Analyses/SupplementaryAnalysis/URD-11-BatchModuleRemovalAndClusteringAnalysisOfSmartseqDataset.Rmd

DESCRIPTION

INSTALL.md

LICENSE

NAMESPACE

NEWS.md R/NMFDoublets.R R/batch.R R/branchpoint-investigation.R R/branchpointPlot.R R/cells.R R/cluster.R R/data-for-plot.R R/diff-exp.R R/diffusion-map.R R/diffusion.R R/dropseq-dge.R R/fetch-data.R R/flood.R R/gene-cascade.R R/gene-smooth.R R/import.R R/impulse.R R/knn.R R/math.R R/pca.R R/plot-cells.R R/plot-dim-3D.R R/plot-dim.R R/plot-genes.R R/pseudotime-stability-plots.R R/subset.R R/tree-force-layout.R R/tree-layout.R R/tree-navigate.R R/tree-plots.R R/tree-structure.R R/tree-tips.R R/tree.R R/tsne.R R/urd-class.R R/urd-package.R R/utils.R R/var-genes.R README.md URD-Install.R

URD.Rproj

man/NMFDoubletsDefineModules.Rd man/NMFDoubletsDetermineCells.Rd man/NMFDoubletsPlotModuleCombos.Rd man/NMFDoubletsPlotModuleThresholds.Rd man/NMFDoubletsPlotModulesInCell.Rd man/URD.Rd man/URDclass.Rd man/allSegmentDivergenceByPseudotime.Rd man/assignCellsToNodes.Rd man/assignCellsToSegments.Rd man/aucprTestAlongTree.Rd man/aucprTestByFactor.Rd man/aucprThreshold.Rd man/batchComBat.Rd man/binomTestAlongTree.Rd man/branchpointDetailsPreferenceDist.Rd man/branchpointDetailsVisitDist.Rd man/branchpointDetailsVisitTsne.Rd man/branchpointPreferenceLayout.Rd man/buildTree.Rd man/calcDM.Rd man/calcKNN.Rd man/calcPCA.Rd man/calcTsne.Rd man/cellDistByExpression.Rd man/cellsAlongLineage.Rd man/cellsInCluster.Rd man/clusterCentroids.Rd man/clusterDE.Rd man/clusterTipPotential.Rd man/collapseShortSegments.Rd man/combine.probs.Rd man/combineSmoothFit.Rd man/combineTipVisitation.Rd man/corner.Rd man/createURD.Rd man/cropSmoothFit.Rd man/cutstring.Rd man/data.for.plot.Rd man/deTTest.Rd man/defaultURDContinuousColors.Rd man/differentialAUCPR.Rd man/divergenceKSVisitation.Rd man/divergencePreferenceDip.Rd man/dsCombineDGE.Rd man/dsCutoffPlot.Rd man/dsMetaTrim.Rd man/dsReadDGE.Rd man/dsReadStats.Rd man/edgesFromDM.Rd man/fdlDensity.Rd man/findVariableGenes.Rd man/floodBuildTM.Rd man/floodPseudotime.Rd man/floodPseudotimeCalc.Rd man/floodPseudotimeProcess.Rd man/geneCascadeHeatmap.Rd man/geneCascadeImpulsePlots.Rd man/geneCascadeProcess.Rd man/geneSmoothFit.Rd man/geneSmoothReduce.Rd man/getBinaryData.Rd man/getUPXData.Rd man/getZData.Rd man/graphClustering.Rd man/gridArrangeMulti.Rd man/groupFromCells.Rd man/importDM.Rd man/impulse.dderiv.double.Rd man/impulse.dderiv.single.Rd man/impulse.deriv.double.Rd man/impulse.deriv.single.Rd man/impulse.double.Rd man/impulse.fit.double.Rd man/impulse.fit.single.Rd man/impulse.single.Rd man/impulse.start.double.Rd man/impulse.start.single.Rd man/impulseFit.Rd man/interpolate.points.Rd man/inv.logistic.Rd man/is.wholenumber.Rd man/knnOutliers.Rd man/loadTipCells.Rd man/logistic.Rd man/markersAUCPR.Rd man/markersBinom.Rd man/matrixReduce.Rd man/mean.of.logs.Rd man/mean.of.logs.pos.Rd man/mean.pos.Rd man/moduleTestAlongTree.Rd man/nameSegments.Rd man/num.mean.Rd man/output.uniform.Rd man/pcSDPlot.Rd man/pcTopGenes.Rd man/pcaMarchenkoPastur.Rd man/plotBranchpoint.Rd man/plotDim.Rd man/plotDim3D.Rd man/plotDim3DStoreView.Rd man/plotDimArray.Rd man/plotDimDiscretized.Rd man/plotDimDual.Rd man/plotDimHighlight.Rd man/plotDists.Rd man/plotDot.Rd man/plotScatter.Rd man/plotSmoothFit.Rd man/plotSmoothFitMultiCascade.Rd man/plotTree.Rd man/plotTreeDiscretized.Rd man/plotTreeDual.Rd man/plotTreeForce.Rd man/plotTreeForce2D.Rd man/plotTreeForceDual.Rd man/plotTreeForceStore3DView.Rd man/plotTreeHighlight.Rd man/plotViolin.Rd man/pmax.abs.Rd man/preference.Rd man/processRandomWalks.Rd man/processRandomWalksFromTips.Rd man/prop.exp.Rd man/prop.nonexp.Rd man/pseudotimeBreakpointByStretch.Rd man/pseudotimeBreakpointByStretchV1.Rd man/pseudotimeDetermineLogistic.Rd man/pseudotimeMovingWindow.Rd man/pseudotimePlotStabilityCells.Rd man/pseudotimePlotStabilityOverall.Rd man/pseudotimePlotVisits.Rd man/pseudotimeWeightTransitionMatrix.Rd man/putativeCellsInSegment.Rd man/reformatSegmentJoins.Rd man/removeUnitarySegments.Rd man/rotateCoords3d.Rd man/segChildren.Rd man/segChildrenAll.Rd man/segParent.Rd man/segParentAll.Rd man/segSiblings.Rd man/segTerminal.Rd man/seuratToURD.Rd man/show.Rd man/simulateRandomWalk.Rd man/simulateRandomWalksFromTips.Rd man/sum.of.logs.Rd man/tipPotential.Rd man/translateCoords3d.Rd man/translateSegmentNames.Rd man/treeForceDirectedLayout.Rd man/treeForcePositionLabels.Rd man/treeForceRotateCoords.Rd man/treeForceStretchCoords.Rd man/treeForceTranslateCoords.Rd man/treeLayoutCells.Rd man/treeLayoutDendrogram.Rd man/treeLayoutElaborate.Rd man/txBarcodesIntegerToChar.Rd man/txCutoffPlot.Rd man/txReadDGE.Rd man/txReadsPerCell.Rd man/urdSubset.Rd man/visitDivergenceByPseudotime.Rd man/whichCells.Rd

farrellja/URD documentation built on June 17, 2020, 4:48 a.m.