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] (
Maintainer: Kelly Street <street.kelly at gmail.com>
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")| Differential Topology: Comparing Conditions along a Trajectory | HTML | R Script |
| Slingshot: Trajectory Inference for Single-Cell Data | HTML | R Script |
| 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 |
| Linking To | |
| Suggests | BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr |
| System Requirements | |
| Enhances | |
| URL | |
| Bug Reports | https://github.com/kstreet13/slingshot/issues |
See More
| 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 |