slingshot

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8

Tools for ordering single-cell sequencing

Bioconductor version: Development (3.24)

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] (ORCID: ORCID: 0000-0003-3641-729X , github: rcannood)

Maintainer: Kelly Street <street.kelly at gmail.com>

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

Kelly Street, Davide Risso, Diya Das. slingshot: Tools for ordering single-cell sequencing. doi:10.18129/B9.bioc.slingshot, R package version 2.21.0, https://bioconductor.org/packages/slingshot.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, DifferentialExpression, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version	2.21.0
In Bioconductor since	BioC 3.8 (R-3.5) (8 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

Suggests	BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr
Linking To
Enhances
Depends On Me	OSCA.advanced
Imports Me	condiments, scRNAseqApp, tradeSeq
Suggests Me	blase, dandelionR, RaceID, scLANE
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	slingshot_2.21.0.tar.gz
Windows Binary (x86_64)	slingshot_2.21.0.zip
macOS Binary (big-sur-x86_64)	slingshot_2.21.0.tgz
macOS Binary (sonoma-arm64)	slingshot_2.21.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/slingshot
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/slingshot
Package Short Url	https://bioconductor.org/packages/slingshot/
Package Downloads Report	Download Stats