recipe bioconductor-cellmigration

Track Cells, Analyze Cell Trajectories and Compute Migration Statistics






Import TIFF images of fluorescently labeled cells, and track cell movements over time. Parallelization is supported for image processing and for fast computation of cell trajectories. In-depth analysis of cell trajectories is enabled by 15 trajectory analysis functions.

package bioconductor-cellmigration

(downloads) docker_bioconductor-cellmigration



depends r-base:


depends r-doparallel:

depends r-factominer:

depends r-fme:

depends r-foreach:

depends r-hmisc:

depends r-matrixstats:

depends r-reshape2:

depends r-sp:

depends r-spatialtools:

depends r-tiff:

depends r-vioplot:



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-cellmigration

and update with::

   mamba update bioconductor-cellmigration

To create a new environment, run:

mamba create --name myenvname bioconductor-cellmigration

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

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