Tools for ordering single-cell sequencing

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Documentation for package ‘slingshot’ version 2.17.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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