Tools for ordering single-cell sequencing


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Documentation for package ‘slingshot’ version 2.16.0

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as.PseudotimeOrdering Conversion to PseudotimeOrdering
as.PseudotimeOrdering-method Conversion to PseudotimeOrdering
as.SlingshotDataSet Conversion to SlingshotDataSet
as.SlingshotDataSet-method Conversion to SlingshotDataSet
embedCurves Embed trajectory in new space
embedCurves-method Embed trajectory in new space
getCurves Construct Simultaneous Principal Curves
getCurves-method Construct Simultaneous Principal Curves
getLineages Infer Lineage Structure from Clustered Samples
getLineages-method Infer Lineage Structure from Clustered Samples
lines.SlingshotDataSet Plot Slingshot output
newSlingshotDataSet Initialize an object of class 'SlingshotDataSet'
newSlingshotDataSet-method Initialize an object of class 'SlingshotDataSet'
pairs-SlingshotDataSet Pairs plot of Slingshot output
pairs.SlingshotDataSet Pairs plot of Slingshot output
plot-method Plot Slingshot output
plot-SlingshotDataSet Plot Slingshot output
plot.SlingshotDataSet Plot Slingshot output
plot3d-SlingshotDataSet Plot Slingshot output in 3D
plot3d.SlingshotDataSet Plot Slingshot output in 3D
predict-method Predict from a Slingshot model
reducedDim-method Class 'SlingshotDataSet'
reducedDims-method Class 'SlingshotDataSet'
show-method Class 'SlingshotDataSet'
slingAvgPseudotime Get Slingshot pseudotime values
slingAvgPseudotime-method Get Slingshot pseudotime values
slingBranchGraph Construct graph of slingshot branch labels
slingBranchGraph-method Construct graph of slingshot branch labels
slingBranchID Get slingshot branch labels
slingBranchID-method Get slingshot branch labels
slingClusterLabels Extract cluster labels used by Slingshot
slingClusterLabels-method Extract cluster labels used by Slingshot
slingCurves Extract simultaneous principal curves
slingCurves-method Extract simultaneous principal curves
slingCurveWeights Get Slingshot pseudotime values
slingCurveWeights-method Get Slingshot pseudotime values
slingLineages Extract the Slingshot lineages
slingLineages-method Extract the Slingshot lineages
slingMST Extract Slingshot minimum spanning tree
slingMST-method Extract Slingshot minimum spanning tree
slingParams Methods for parameters used by Slingshot
slingParams-method Methods for parameters used by Slingshot
slingPseudotime Get Slingshot pseudotime values
slingPseudotime-method Get Slingshot pseudotime values
slingReducedDim Extract dimensionality reduction used by Slingshot
slingReducedDim-method Extract dimensionality reduction used by Slingshot
slingshot Perform trajectory inference with Slingshot
slingshot-method Perform trajectory inference with Slingshot
SlingshotDataSet Extract Slingshot output
SlingshotDataSet-class Class 'SlingshotDataSet'
SlingshotDataSet-method Extract Slingshot output
slingshotExample Bifurcating lineages data