DOI: 10.18129/B9.bioc.slingshot  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see slingshot.

Tools for ordering single-cell sequencing

Bioconductor version: 3.16

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.

Author: Kelly Street [aut, cre, cph], Davide Risso [aut], Diya Das [aut], Sandrine Dudoit [ths], Koen Van den Berge [ctb], Robrecht Cannoodt [ctb] (, rcannood)

Maintainer: Kelly Street <street.kelly at>

Citation (from within R, enter citation("slingshot")):


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HTML R Script Differential Topology: Comparing Conditions along a Trajectory
HTML R Script Slingshot: Trajectory Inference for Single-Cell Data
PDF   Reference Manual


biocViews Clustering, DifferentialExpression, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 2.6.0
In Bioconductor since BioC 3.8 (R-3.5) (4.5 years)
License Artistic-2.0
Depends R (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils
Imports graphics, grDevices, igraph, matrixStats, methods, S4Vectors, SingleCellExperiment, SummarizedExperiment
Suggests BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr
Depends On Me OSCA.advanced
Imports Me condiments, tradeSeq, traviz
Suggests Me Platypus, RaceID
Links To Me
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