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>

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

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

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