recipe bioconductor-trajectoryutils

Single-Cell Trajectory Analysis Utilities






Implements low-level utilities for single-cell trajectory analysis, primarily intended for re-use inside higher-level packages. Include a function to create a cluster-level minimum spanning tree and data structures to hold pseudotime inference results.

package bioconductor-trajectoryutils

(downloads) docker_bioconductor-trajectoryutils



depends bioconductor-s4vectors:


depends bioconductor-singlecellexperiment:


depends bioconductor-summarizedexperiment:


depends r-base:


depends r-igraph:

depends r-matrix:



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-trajectoryutils

and update with::

   mamba update bioconductor-trajectoryutils

To create a new environment, run:

mamba create --name myenvname bioconductor-trajectoryutils

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-trajectoryutils/tags`_ for valid values for ``<tag>``)

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