API for farrellja/URD
URD

Global functions
URD Man page Man page
URD-package Man page 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
combineTipVisitation Man page Source code
corner Man page Source code
createURD 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 Source code
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
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.double Man page Source code
impulse.fit.double Man page Source code
impulse.fit.single Man page Source code
impulse.llrtest 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
llrtest.dof Man page Source code
loadTipCells Man page Source code
log.likelihood.ratio Man page Source code
logistic Man page Source code
markersAUCPR Man page Source code
markersBinom 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
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
plotTree Man page Source code
plotTreeForce Man page Source code
plotTreeForce2D Man page Source code
plotTreeForceDual Man page Source code
plotTreeForceStore3DView 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
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 Man page Source code 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 Source code
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
farrellja/URD documentation built on Oct. 5, 2018, 1:24 a.m.