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Tools for ordering single-cell sequencing

Bioconductor version: Release (3.19)

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews Clustering, DifferentialExpression, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 2.12.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License Artistic-2.0
Depends R (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils
Imports graphics, grDevices, igraph, matrixStats, methods, S4Vectors, SingleCellExperiment, SummarizedExperiment
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Suggests BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr
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Depends On Me OSCA.advanced
Imports Me condiments, scRNAseqApp, tradeSeq, traviz
Suggests Me RaceID
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Follow Installation instructions to use this package in your R session.

Source Package slingshot_2.12.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) slingshot_2.12.0.tgz
macOS Binary (arm64) slingshot_2.12.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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