recipe bioconductor-slingshot

Tools for ordering single-cell sequencing






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.

package bioconductor-slingshot

(downloads) docker_bioconductor-slingshot



depends bioconductor-s4vectors:


depends bioconductor-singlecellexperiment:


depends bioconductor-summarizedexperiment:


depends bioconductor-trajectoryutils:


depends r-base:


depends r-igraph:

depends r-matrixstats:

depends r-princurve:




You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-slingshot

and update with::

   mamba update bioconductor-slingshot

To create a new environment, run:

mamba create --name myenvname bioconductor-slingshot

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-slingshot/tags`_ for valid values for ``<tag>``)

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