Man pages for farrellja/URD
URD

allSegmentDivergenceByPseudotimeAll Segment Divergence By Pseudotime
assignCellsToNodesAssign Cells to Nodes
assignCellsToSegmentsAssign Cells to Segments
aucprTestAlongTreeTest for differential gene expression along tree using...
aucprTestByFactorTest for differential gene expression along tree using...
aucprThresholdPrecision-Recall AUC threshold
batchComBatBatch correct data using ComBat
binomTestAlongTreeTest for differential gene expression along tree using...
branchpointDetailsPreferenceDistInvestigate Branchpoint - Visit Preference Distributions
branchpointDetailsVisitDistInvestigate Branchpoint - Visit Frequency Distributions
branchpointDetailsVisitTsneInvestigate Branchpoint - tSNE Visitation Groups
branchpointPreferenceLayoutGenerate Branchpoint Preference Layout
buildTreeBuild Tree
calcDMCalculate a diffusion map
calcKNNCalculate k-nearest neighbor graph
calcPCACalculate principal components
calcTsneCalculate tSNE projection of data
cellDistByExpressionCalculates the distance matrix between cells given their gene...
cellsAlongLineageExtract cells along a lineage pathway
cellsInClusterReturn names of cells in a given cluster
clusterCentroidsCluster centroids in gene expression space
clusterDECluster Differential Expression
clusterTipPotentialTip Potential of Clusters
collapseShortSegmentsCollapse Short Segments
combine.probsCombine probabilities
combineTipVisitationCombine Tip Visitation
cornerCorner of data frame or matrix
createURDCreate a new URD object
data.for.plotRetrieve data for plotting
defaultURDContinuousColorsDefault URD continuous colors
deTTestt-Test for Differential Expression
differentialAUCPRArea under precision-recall curve for determining marker...
divergenceKSVisitationCalculate visitation divergence using KS-test
divergencePreferenceDipCalculate visitation divergence based on bimodality of...
dsCombineDGEFuse Dropseq Digital Gene Expression tables
dsCutoffPlotPlot Cumulative Distribution of Reads per Cell Barcode
dsMetaTrimPlot and trim Dropseq DGE tables by metadata
dsReadDGERead Dropseq Digital Gene Expression tables
dsReadStatsRead cell barcode statistics produced by Dropseq pipeline
edgesFromDMCreate an edge list from the transition matrix of the...
fdlDensityCalculate force-directed layout local density
findVariableGenesFind variable genes
floodBuildTMBuild pseudotime transition matrix
floodPseudotimeCalculate pseudotime by 'flooding'
floodPseudotimeCalcA single iteration of flood pseudotime calculation.
floodPseudotimeProcessProcess Flood Pseudotime
geneCascadeHeatmapPlot Gene Cascade Heatmap
geneCascadeImpulsePlotsPlot Impulse Fits For a Gene Cascade
geneCascadeProcessProcess a gene cascade
getBinaryDataGet binary data
getUPXDataGet UPX (un-logged) data
getZDataGet z-scored data
graphClusteringSpectral Graph Clustering
gridArrangeMultiArrange multiple ggplots into several gridded pages
groupFromCellsCreate a group.id from a list of cells
importDMImport a pre-calculated diffusion map
impulse.doubleEvaluate the impulse model (double sigmoid) function, given...
impulseFitFit gene expression data with an impulse model
impulse.fit.doubleFit Impulse Model (Double sigmoid)
impulse.fit.singleFit Impulse Model (Single sigmoid)
impulse.llrtestLog likelihood ratio test for impulse fits
impulse.singleEvaluate the impulse model (single sigmoid) function, given...
impulse.start.doubleStarting Conditions for impulse model (double sigmoid)
impulse.start.singleStarting Conditions for impulse model (single sigmoid)
interpolate.pointsInterpolate dimensionality reduction dimensions
inv.logisticInverse logistic function
is.wholenumberCheck whether input is a whole number
knnOutliersFind outliers in terms of their distance in the k-nearest...
llrtest.dofLog likelihood ratio test for impulse fits
loadTipCellsLoad Tip Cells
logisticLogistic function
log.likelihood.ratioLog-likelihood ratio test
markersAUCPRTest for markers of a population using a precision-recall...
markersBinomTest for differential gene expression in two populations...
mean.of.logsArithmetic mean of log-transformed values
mean.of.logs.posArithmetic mean of positive log-transformed values
mean.posMean of positive values
moduleTestAlongTreeDifferential NMF module expression testing along tree
nameSegmentsName Segments
num.meanArithmetic Mean of As Numeric
output.uniformIs Vector Uniform?
pcaMarchenkoPasturMarchenko-Pastur Significant PCs
pcSDPlotPC Standard Deviation Plot
pcTopGenesPC Top Loaded Genes
plotBranchpointPlot Data On Branchpoint Layout
plotDimDimensionality Reduction Plot
plotDim3DDimensionality reduction plot in 3D.
plotDim3DStoreViewStore a 3D view for plotDim3D
plotDimArrayDimensionality Reduction Plot Array
plotDimDualDimensionality Reduction Plot (Dual Color)
plotDimHighlightDimensionality Reduction Plot With Highlighted Clusters
plotDistsPlot distributions
plotDotDot Plot
plotScatterGene Expression Scatterplot
plotTreePlot 2D Dendrogram of URD Tree
plotTreeForcePlot force-directed layout of tree
plotTreeForce2DPlot tree force-directed layout in 2D
plotTreeForceDualPlot force-directed layout of tree
plotTreeForceStore3DViewStore a 3D view for force-directed layouts
plotViolinViolin plot of gene expression
pmax.absReturn the signed value with greater magnitude
preferenceDetermining preference between a pair of values
processRandomWalksProcess random walks into visitation frequency
processRandomWalksFromTipsProcess random walks from all tips
prop.expReturns proportion of expressing cells
prop.nonexpReturns proportion of non-expressing cells
pseudotimeBreakpointByStretchPseudotime Breakpoint By Stretch
pseudotimeBreakpointByStretchV1Find Pseudotime Breakpoint
pseudotimeDetermineLogisticDetermine logistic parameters for biasing transition matrix
pseudotimeMovingWindowMoving window through pseudotime
pseudotimePlotStabilityCellsPlot Pseudotime Stability (Individual Cells)
pseudotimePlotStabilityOverallPlot Pseudotime Stability
pseudotimePlotVisitsPlot Cell Visitation By Random Walks or Flood Pseudotime
pseudotimeWeightTransitionMatrixWeight transition matrix by pseudotime
putativeCellsInSegmentPutative Cells in Segment
reformatSegmentJoinsReformat Segment Joins
removeUnitarySegmentsRemove Unitary Segments
rotateCoords3dRotate coordinates in 3D
segChildrenDirect children of Segment
segChildrenAllAll children of segment
segParentParent of segment
segParentAllAll Upstream Segments
segSiblingsSiblings of segments
segTerminalGet all terminal segments from a tree
seuratToURDImport URD from Seurat
showURD show method
simulateRandomWalkSimulate random walks
simulateRandomWalksFromTipsSimulate Random Walks From All Tips
sum.of.logsSum of log-transformed values
tipPotentialFind tip potential
translateCoords3dTranslate coordinates in 3D
translateSegmentNamesTranslate Segment Names
treeForceDirectedLayoutGenerate force-directed layout using tip-walk data.
treeForcePositionLabelsDetermine position for segment labels in force-directed...
treeForceRotateCoordsRotate points in force-directed layout
treeForceStretchCoordsStretch points in force-directed layout
treeForceTranslateCoordsTranslate points in force-directed layout
treeLayoutCellsAdd cells to tree layout
treeLayoutDendrogramLayout Tree Dendrogram
treeLayoutElaborateElaborate Tree Dendrogram With Nodes
txBarcodesIntegerToCharConvert 10X Integer-stored barcodes to character ones for...
txCutoffPlotPlot Cumulative Distribution of Reads per Cell Barcode
txReadDGERead in Digital Gene Expression Matrix from 10X Cellranger
txReadsPerCellRead 10X Reads per Cell barcode
URDURD - Reconstruction of Branching Developmental Trajectories
URDclassURD class
urdSubsetSubset an URD object
visitDivergenceByPseudotimeVisitation Divergence for Pseudotime Windows
farrellja/URD documentation built on Oct. 5, 2018, 1:24 a.m.