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