Package: slingshot 2.15.0
Kelly Street
slingshot: Tools for ordering single-cell sequencing
Provides functions for inferring continuous, branching lineage structures in low-dimensional data. Slingshot was designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering. It is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.
Authors:
slingshot_2.15.0.tar.gz
slingshot_2.15.0.zip(r-4.5)slingshot_2.15.0.zip(r-4.4)slingshot_2.15.0.zip(r-4.3)
slingshot_2.15.0.tgz(r-4.4-any)slingshot_2.15.0.tgz(r-4.3-any)
slingshot_2.15.0.tar.gz(r-4.5-noble)slingshot_2.15.0.tar.gz(r-4.4-noble)
slingshot_2.15.0.tgz(r-4.4-emscripten)slingshot_2.15.0.tgz(r-4.3-emscripten)
slingshot.pdf |slingshot.html✨
slingshot/json (API)
| # Install 'slingshot' in R: |
| install.packages('slingshot', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kstreet13/slingshot/issues
- slingshotExample - Bifurcating lineages data
On BioConductor:slingshot-2.15.0(bioc 3.21)slingshot-2.14.0(bioc 3.20)
clusteringdifferentialexpressiongeneexpressionrnaseqsequencingsoftwaresinglecelltranscriptomicsvisualization
Last updated 23 days agofrom:cf41eecefb. Checks:OK: 2 NOTE: 2 WARNING: 3. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | WARNING | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 31 2024 |
| R-4.4-win | WARNING | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | WARNING | Oct 31 2024 |
| R-4.3-mac | OK | Oct 31 2024 |
Exports:as.PseudotimeOrderingas.SlingshotDataSetembedCurvesgetCurvesgetLineagesnewSlingshotDataSetplot3d.SlingshotDataSetpredictreducedDimreducedDimsshowslingAvgPseudotimeslingBranchGraphslingBranchIDslingClusterLabelsslingCurvesslingCurveWeightsslingLineagesslingMSTslingParamsslingPseudotimeslingReducedDimslingshotSlingshotDataSet
Dependencies:abindaskpassBiobaseBiocGenericsclicpp11crayoncurlDelayedArrayGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrigraphIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpkgconfigprincurveR6RcpprlangS4ArraysS4VectorsSingleCellExperimentSparseArraySummarizedExperimentsysTrajectoryUtilsUCSC.utilsvctrsXVectorzlibbioc
Differential Topology: Comparing Conditions along a Trajectory
Rendered fromconditionsVignette.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2021-03-22
Started: 2019-08-21
Slingshot: Trajectory Inference for Single-Cell Data
Rendered fromvignette.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2023-03-29
Started: 2019-04-23
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Conversion to PseudotimeOrdering | as.PseudotimeOrdering as.PseudotimeOrdering,PseudotimeOrdering-method as.PseudotimeOrdering,SingleCellExperiment-method as.PseudotimeOrdering,SlingshotDataSet-method |
| Conversion to SlingshotDataSet | as.SlingshotDataSet as.SlingshotDataSet,PseudotimeOrdering-method as.SlingshotDataSet,SingleCellExperiment-method as.SlingshotDataSet,SlingshotDataSet-method |
| Embed trajectory in new space | embedCurves embedCurves,PseudotimeOrdering,matrix-method embedCurves,SingleCellExperiment,character-method embedCurves,SingleCellExperiment,matrix-method |
| Construct Simultaneous Principal Curves | getCurves getCurves,PseudotimeOrdering-method getCurves,SingleCellExperiment-method getCurves,SlingshotDataSet-method |
| Infer Lineage Structure from Clustered Samples | getLineages getLineages,data.frame,ANY-method getLineages,matrix,ANY-method getLineages,matrix,character-method getLineages,matrix,factor-method getLineages,matrix,matrix-method getLineages,matrix,numeric-method getLineages,PseudotimeOrdering,ANY-method getLineages,SingleCellExperiment,ANY-method getLineages,SlingshotDataSet,ANY-method |
| Initialize an object of class 'SlingshotDataSet' | newSlingshotDataSet newSlingshotDataSet,data.frame,ANY-method newSlingshotDataSet,matrix,ANY-method newSlingshotDataSet,matrix,character-method newSlingshotDataSet,matrix,factor-method newSlingshotDataSet,matrix,matrix-method newSlingshotDataSet,matrix,numeric-method |
| Pairs plot of Slingshot output | pairs-SlingshotDataSet pairs.SlingshotDataSet |
| Plot Slingshot output | lines.SlingshotDataSet plot,SlingshotDataSet,ANY-method plot-SlingshotDataSet plot.SlingshotDataSet |
| Plot Slingshot output in 3D | plot3d-SlingshotDataSet plot3d.SlingshotDataSet |
| Predict from a Slingshot model | predict,PseudotimeOrdering-method predict,SlingshotDataSet-method |
| Construct graph of slingshot branch labels | slingBranchGraph slingBranchGraph,ANY-method |
| Get slingshot branch labels | slingBranchID slingBranchID,ANY-method |
| Extract cluster labels used by Slingshot | slingClusterLabels slingClusterLabels,PseudotimeOrdering-method slingClusterLabels,SingleCellExperiment-method slingClusterLabels,SlingshotDataSet-method |
| Extract simultaneous principal curves | slingCurves slingCurves,PseudotimeOrdering-method slingCurves,SingleCellExperiment-method slingCurves,SlingshotDataSet-method |
| Extract the Slingshot lineages | slingLineages slingLineages,PseudotimeOrdering-method slingLineages,SingleCellExperiment-method slingLineages,SlingshotDataSet-method |
| Extract Slingshot minimum spanning tree | slingMST slingMST,PseudotimeOrdering-method slingMST,SingleCellExperiment-method slingMST,SlingshotDataSet-method |
| Methods for parameters used by Slingshot | slingParams slingParams,PseudotimeOrdering-method slingParams,SingleCellExperiment-method slingParams,SlingshotDataSet-method |
| Get Slingshot pseudotime values | slingAvgPseudotime slingAvgPseudotime,ANY-method slingCurveWeights slingCurveWeights,PseudotimeOrdering-method slingCurveWeights,SingleCellExperiment-method slingCurveWeights,SlingshotDataSet-method slingPseudotime slingPseudotime,PseudotimeOrdering-method slingPseudotime,SingleCellExperiment-method slingPseudotime,SlingshotDataSet-method |
| Extract dimensionality reduction used by Slingshot | slingReducedDim slingReducedDim,PseudotimeOrdering-method slingReducedDim,SingleCellExperiment-method slingReducedDim,SlingshotDataSet-method |
| Perform trajectory inference with Slingshot | slingshot slingshot,ClusterExperiment,ANY-method slingshot,data.frame,ANY-method slingshot,matrix,ANY-method slingshot,matrix,character-method slingshot,matrix,factor-method slingshot,matrix,matrix-method slingshot,matrix,numeric-method slingshot,SingleCellExperiment,ANY-method slingshot,SlingshotDataSet,ANY-method |
| Extract Slingshot output | SlingshotDataSet SlingshotDataSet,PseudotimeOrdering-method SlingshotDataSet,SingleCellExperiment-method SlingshotDataSet,SlingshotDataSet-method |
| Class 'SlingshotDataSet' | reducedDim,SlingshotDataSet,ANY-method reducedDims,SlingshotDataSet-method show,SlingshotDataSet-method SlingshotDataSet-class |
| Bifurcating lineages data | slingshotExample |
