# Tools for ordering single-cell sequencing

## Documentation for package ‘slingshot’ version 2.0.0

- 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'
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