recipe bioconductor-fusesom

A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets






A correlation-based multiview self-organizing map for the characterization of cell types in highly multiplexed in situ imaging cytometry assays (`FuseSOM`) is a tool for unsupervised clustering. `FuseSOM` is robust and achieves high accuracy by combining a `Self Organizing Map` architecture and a `Multiview` integration of correlation based metrics. This allows FuseSOM to cluster highly multiplexed in situ imaging cytometry assays.

package bioconductor-fusesom

(downloads) docker_bioconductor-fusesom



depends bioconductor-s4vectors:


depends bioconductor-s4vectors:


depends bioconductor-summarizedexperiment:


depends bioconductor-summarizedexperiment:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends libstdcxx-ng:


depends r-analogue:

depends r-base:


depends r-cluster:

depends r-coop:

depends r-diptest:

depends r-fastcluster:

depends r-fcps:

depends r-fpc:

depends r-ggplot2:

depends r-ggplotify:

depends r-ggpubr:

depends r-pheatmap:

depends r-proxy:

depends r-psych:

depends r-rcpp:

depends r-stringr:



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-fusesom

and update with::

   mamba update bioconductor-fusesom

To create a new environment, run:

mamba create --name myenvname bioconductor-fusesom

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

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