slingshot

DOI: 10.18129/B9.bioc.slingshot  

Tools for ordering single-cell sequencing

Bioconductor version: Release (3.17)

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

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

Details

biocViews	Clustering, DifferentialExpression, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version	2.8.0
In Bioconductor since	BioC 3.8 (R-3.5) (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
LinkingTo
Suggests	BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr
SystemRequirements
Enhances
URL
BugReports	https://github.com/kstreet13/slingshot/issues
Depends On Me	OSCA.advanced
Imports Me	condiments, scRNAseqApp, tradeSeq, traviz
Suggests Me	RaceID
Links To Me
Build Report

Package Archives

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

Source Package	slingshot_2.8.0.tar.gz
Windows Binary	slingshot_2.8.0.zip
macOS Binary (x86_64)	slingshot_2.8.0.tgz
macOS Binary (arm64)	slingshot_2.8.0.tgz
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
Old Source Packages for BioC 3.17	Source Archive