slingshot

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see slingshot.

Tools for ordering single-cell sequencing


Bioconductor version: 3.10

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]

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

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

Installation

To install this package, start R (version "3.6") 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")
Differential Topology HTML R Script
Slingshot HTML R Script
Reference Manual PDF

Details

biocViews Clustering, DifferentialExpression, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.4.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License Artistic-2.0
Depends R (>= 3.5), princurve (>= 2.0.4), stats
Imports ape, graphics, grDevices, igraph, matrixStats, methods, SingleCellExperiment, SummarizedExperiment
System Requirements
URL
Bug Reports https://github.com/kstreet13/slingshot/issues
See More
Suggests BiocGenerics, BiocStyle, clusterExperiment, destiny, gam, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, covr
Linking To
Enhances
Depends On Me
Imports Me tradeSeq
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package slingshot_1.4.0.tar.gz
Windows Binary slingshot_1.4.0.zip
Mac OS X 10.11 (El Capitan) slingshot_1.4.0.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 3.10 Source Archive