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slingshot

This is the development version of slingshot; for the stable release version, see slingshot.

Tools for ordering single-cell sequencing


Bioconductor version: Development (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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("slingshot")

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

Documentation

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

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

Details

biocViews Clustering, DifferentialExpression, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 2.11.0
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
System Requirements
URL
Bug Reports https://github.com/kstreet13/slingshot/issues
See More
Suggests BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr
Linking To
Enhances
Depends On Me
Imports Me condiments, scRNAseqApp, tradeSeq, traviz
Suggests Me Platypus, RaceID
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package slingshot_2.11.0.tar.gz
Windows Binary slingshot_2.11.0.zip (64-bit only)
macOS Binary (x86_64) slingshot_2.11.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/slingshot
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/slingshot
Bioc Package Browser https://code.bioconductor.org/browse/slingshot/
Package Short Url https://bioconductor.org/packages/slingshot/
Package Downloads Report Download Stats