recipe bioconductor-celltrails

Reconstruction, visualization and analysis of branching trajectories






CellTrails is an unsupervised algorithm for the de novo chronological ordering, visualization and analysis of single-cell expression data. CellTrails makes use of a geometrically motivated concept of lower-dimensional manifold learning, which exhibits a multitude of virtues that counteract intrinsic noise of single cell data caused by drop-outs, technical variance, and redundancy of predictive variables. CellTrails enables the reconstruction of branching trajectories and provides an intuitive graphical representation of expression patterns along all branches simultaneously. It allows the user to define and infer the expression dynamics of individual and multiple pathways towards distinct phenotypes.

package bioconductor-celltrails

(downloads) docker_bioconductor-celltrails



depends bioconductor-biobase:


depends bioconductor-biocgenerics:


depends bioconductor-singlecellexperiment:


depends bioconductor-summarizedexperiment:


depends r-base:


depends r-cba:

depends r-dendextend:

depends r-dtw:

depends r-envstats:

depends r-ggplot2:

depends r-ggrepel:

depends r-igraph:

depends r-maptree:

depends r-mgcv:

depends r-reshape2:

depends r-rtsne:



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-celltrails

and update with::

   mamba update bioconductor-celltrails

To create a new environment, run:

mamba create --name myenvname bioconductor-celltrails

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

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