slingshot

DOI: 10.18129/B9.bioc.slingshot    

Tools for ordering single-cell sequencing

Bioconductor version: Release (3.8)

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 "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("slingshot", version = "3.8")

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 slingshot Vignette
PDF   Reference Manual

Details

biocViews Clustering, DifferentialExpression, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.0.0
License Artistic-2.0
Depends R (>= 3.5), princurve (>= 2.0.4), stats
Imports ape, clusterExperiment, graphics, grDevices, igraph, matrixStats, methods, rgl, SingleCellExperiment, SummarizedExperiment
LinkingTo
Suggests BiocGenerics, destiny, gam, knitr, mclust, RColorBrewer, rmarkdown, splatter, testthat, covr
SystemRequirements
Enhances
URL
BugReports https://github.com/kstreet13/slingshot/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package slingshot_1.0.0.tar.gz
Windows Binary slingshot_1.0.0.zip
Mac OS X 10.11 (El Capitan) slingshot_1.0.0.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 http://bioconductor.org/packages/slingshot/
Package Downloads Report Download Stats

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