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Bioconductor - slingshot

slingshot

This is the released version of slingshot; for the devel version, see slingshot.

Tools for ordering single-cell sequencing

Bioconductor version: Release (3.21)

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")): Installation

To install this package, start R (version "4.5") 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 PDF Details biocViews Clustering, DifferentialExpression, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization Version 2.16.0 In Bioconductor since BioC 3.8 (R-3.5) (6.5 years) License Artistic-2.0 Depends R (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils Imports graphics, grDevices, igraph, matrixStats, methods, S4Vectors, SingleCellExperiment, SummarizedExperiment System Requirements URL Bug Reports https://github.com/kstreet13/slingshot/issues See More 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 Platypus, RaceID Links To Me Build Report Build Report Package Archives

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

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