Man pages for farrellja/URD
URD
| allSegmentDivergenceByPseudotime | All Segment Divergence By Pseudotime |
| assignCellsToNodes | Assign Cells to Nodes |
| assignCellsToSegments | Assign Cells to Segments |
| aucprTestAlongTree | Test for differential gene expression along tree using... |
| aucprTestByFactor | Test for differential gene expression along tree using... |
| aucprThreshold | Precision-Recall AUC threshold |
| batchComBat | Batch correct data using ComBat |
| binomTestAlongTree | Test for differential gene expression along tree using... |
| branchpointDetailsPreferenceDist | Investigate Branchpoint - Visit Preference Distributions |
| branchpointDetailsVisitDist | Investigate Branchpoint - Visit Frequency Distributions |
| branchpointDetailsVisitTsne | Investigate Branchpoint - tSNE Visitation Groups |
| branchpointPreferenceLayout | Generate Branchpoint Preference Layout |
| buildTree | Build Tree |
| calcDM | Calculate a diffusion map |
| calcKNN | Calculate k-nearest neighbor graph |
| calcPCA | Calculate principal components |
| calcTsne | Calculate tSNE projection of data |
| cellDistByExpression | Calculates the distance matrix between cells given their gene... |
| cellsAlongLineage | Extract cells along a lineage pathway |
| cellsInCluster | Return names of cells in a given cluster |
| clusterCentroids | Cluster centroids in gene expression space |
| clusterDE | Cluster Differential Expression |
| clusterTipPotential | Tip Potential of Clusters |
| collapseShortSegments | Collapse Short Segments |
| combine.probs | Combine probabilities |
| combineSmoothFit | Gene Smooth: Combine smoothed fits |
| combineTipVisitation | Combine Tip Visitation |
| corner | Corner of data frame or matrix |
| createURD | Create a new URD object |
| cropSmoothFit | Gene Smooth: Crop to particular pseudotimes |
| cutstring | Cut string into fields |
| data.for.plot | Retrieve data for plotting |
| defaultURDContinuousColors | Default URD continuous colors |
| deTTest | t-Test for Differential Expression |
| differentialAUCPR | Area under precision-recall curve for determining marker... |
| divergenceKSVisitation | Calculate visitation divergence using KS-test |
| divergencePreferenceDip | Calculate visitation divergence based on bimodality of... |
| dsCombineDGE | Fuse Dropseq Digital Gene Expression tables |
| dsCutoffPlot | Plot Cumulative Distribution of Reads per Cell Barcode |
| dsMetaTrim | Plot and trim Dropseq DGE tables by metadata |
| dsReadDGE | Read Dropseq Digital Gene Expression tables |
| dsReadStats | Read cell barcode statistics produced by Dropseq pipeline |
| edgesFromDM | Create an edge list from the transition matrix of the... |
| fdlDensity | Calculate force-directed layout local density |
| findVariableGenes | Find variable genes |
| floodBuildTM | Build pseudotime transition matrix |
| floodPseudotime | Calculate pseudotime by 'flooding' |
| floodPseudotimeCalc | A single iteration of flood pseudotime calculation. |
| floodPseudotimeProcess | Process Flood Pseudotime |
| geneCascadeHeatmap | Plot Gene Cascade Heatmap |
| geneCascadeImpulsePlots | Plot Impulse Fits For a Gene Cascade |
| geneCascadeProcess | Gene Cascade: Fit expression of genes |
| geneSmoothFit | Gene Smooth: Fit expression of genes |
| geneSmoothReduce | Gene Smooth: Reduce dimensions of Smooth Fit |
| getBinaryData | Get binary data |
| getUPXData | Get UPX (un-logged) data |
| getZData | Get z-scored data |
| graphClustering | Spectral Graph Clustering |
| gridArrangeMulti | Arrange multiple ggplots into several gridded pages |
| groupFromCells | Create a group.id from a list of cells |
| importDM | Import a pre-calculated diffusion map |
| impulse.dderiv.double | Second derivative of double sigmoid ("impulse") |
| impulse.dderiv.single | Second derivative of single sigmoid |
| impulse.deriv.double | Single derivative of double sigmoid ("impulse") |
| impulse.deriv.single | Derivative of single sigmoid |
| impulse.double | Evaluate the impulse model (double sigmoid) function, given... |
| impulseFit | Fit gene expression data with an impulse model |
| impulse.fit.double | Fit Impulse Model (Double sigmoid) |
| impulse.fit.single | Fit Single Sigmoid Model |
| impulse.single | Evaluate the impulse model (single sigmoid) function, given... |
| impulse.start.double | Starting Conditions for Impulse Model (double sigmoid) |
| impulse.start.single | Starting conditions for single sigmoid model |
| interpolate.points | Interpolate dimensionality reduction dimensions |
| inv.logistic | Inverse logistic function |
| is.wholenumber | Check whether input is a whole number |
| knnOutliers | Find outliers in terms of their distance in the k-nearest... |
| loadTipCells | Load Tip Cells |
| logistic | Logistic function |
| markersAUCPR | Test for markers of a population using a precision-recall... |
| markersBinom | Test for differential gene expression in two populations... |
| matrixReduce | Reduce matrix |
| mean.of.logs | Arithmetic mean of log-transformed values |
| mean.of.logs.pos | Arithmetic mean of positive log-transformed values |
| mean.pos | Mean of positive values |
| moduleTestAlongTree | Differential NMF module expression testing along tree |
| nameSegments | Name Segments |
| NMFDoubletsDefineModules | NMF Doublets: Calculate module pair overlap |
| NMFDoubletsDetermineCells | NMF Doublets: Identify cells that express non-overlapping NMF... |
| NMFDoubletsPlotModuleCombos | Plot NMF module combinations and dual-expressing cells |
| NMFDoubletsPlotModulesInCell | Plot cells' expression of modules |
| NMFDoubletsPlotModuleThresholds | NMF Doublets: Plot module overlaps |
| num.mean | Arithmetic Mean of As Numeric |
| output.uniform | Is Vector Uniform? |
| pcaMarchenkoPastur | Marchenko-Pastur Significant PCs |
| pcSDPlot | PC Standard Deviation Plot |
| pcTopGenes | PC Top Loaded Genes |
| plotBranchpoint | Plot Data On Branchpoint Layout |
| plotDim | Dimensionality Reduction Plot |
| plotDim3D | Dimensionality reduction plot in 3D. |
| plotDim3DStoreView | Store a 3D view for plotDim3D |
| plotDimArray | Dimensionality Reduction Plot Array |
| plotDimDiscretized | Dimensionality Reduction Plot (Multi-Color, Discretized) |
| plotDimDual | Dimensionality Reduction Plot (Dual Color) |
| plotDimHighlight | Dimensionality Reduction Plot With Highlighted Clusters |
| plotDists | Plot distributions |
| plotDot | Dot Plot |
| plotScatter | Gene Expression Scatterplot |
| plotSmoothFit | Gene Smooth: Plot a single fit |
| plotSmoothFitMultiCascade | Gene Smooth: Plot multiple fits |
| plotTree | Plot 2D Dendrogram of URD Tree |
| plotTreeDiscretized | Plot 2D Dendrogram of URD Tree, Discretized |
| plotTreeDual | Plot 2D Dendrogram of URD Tree |
| plotTreeForce | Plot force-directed layout of tree |
| plotTreeForce2D | Plot tree force-directed layout in 2D |
| plotTreeForceDual | Plot force-directed layout of tree |
| plotTreeForceStore3DView | Store a 3D view for force-directed layouts |
| plotTreeHighlight | Plot 2D Dendrogram of URD Tree (with cells that meet... |
| plotViolin | Violin plot of gene expression |
| pmax.abs | Return the signed value with greater magnitude |
| preference | Determining preference between a pair of values |
| processRandomWalks | Process random walks into visitation frequency |
| processRandomWalksFromTips | Process random walks from all tips |
| prop.exp | Returns proportion of expressing cells |
| prop.nonexp | Returns proportion of non-expressing cells |
| pseudotimeBreakpointByStretch | Pseudotime Breakpoint By Stretch |
| pseudotimeBreakpointByStretchV1 | Find Pseudotime Breakpoint |
| pseudotimeDetermineLogistic | Determine logistic parameters for biasing transition matrix |
| pseudotimeMovingWindow | Moving window through pseudotime |
| pseudotimePlotStabilityCells | Plot Pseudotime Stability (Individual Cells) |
| pseudotimePlotStabilityOverall | Plot Pseudotime Stability |
| pseudotimePlotVisits | Plot Cell Visitation By Random Walks or Flood Pseudotime |
| pseudotimeWeightTransitionMatrix | Weight transition matrix by pseudotime |
| putativeCellsInSegment | Putative Cells in Segment |
| reformatSegmentJoins | Reformat Segment Joins |
| removeUnitarySegments | Remove Unitary Segments |
| rotateCoords3d | Rotate coordinates in 3D |
| segChildren | Direct children of Segment |
| segChildrenAll | All children of segment |
| segParent | Parent of segment |
| segParentAll | All Upstream Segments |
| segSiblings | Siblings of segments |
| segTerminal | Get all terminal segments from a tree |
| seuratToURD | Import URD from Seurat |
| show | URD show method |
| simulateRandomWalk | Simulate random walks |
| simulateRandomWalksFromTips | Simulate Random Walks From All Tips |
| sum.of.logs | Sum of log-transformed values |
| tipPotential | Find tip potential |
| translateCoords3d | Translate coordinates in 3D |
| translateSegmentNames | Translate Segment Names |
| treeForceDirectedLayout | Generate force-directed layout using tip-walk data. |
| treeForcePositionLabels | Determine position for segment labels in force-directed... |
| treeForceRotateCoords | Rotate points in force-directed layout |
| treeForceStretchCoords | Stretch points in force-directed layout |
| treeForceTranslateCoords | Translate points in force-directed layout |
| treeLayoutCells | Add cells to tree layout |
| treeLayoutDendrogram | Layout Tree Dendrogram |
| treeLayoutElaborate | Elaborate Tree Dendrogram With Nodes |
| txBarcodesIntegerToChar | Convert 10X Integer-stored barcodes to character ones for... |
| txCutoffPlot | Plot Cumulative Distribution of Reads per Cell Barcode |
| txReadDGE | Read in Digital Gene Expression Matrix from 10X Cellranger |
| txReadsPerCell | Read 10X Reads per Cell barcode |
| URD | URD - Reconstruction of Branching Developmental Trajectories |
| URDclass | URD class |
| urdSubset | Subset an URD object |
| visitDivergenceByPseudotime | Visitation Divergence for Pseudotime Windows |
| whichCells | Which cells |
