recipe bioconductor-fusesom

A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/FuseSOM.html

License:

GPL-2

Recipe:

/bioconductor-fusesom/meta.yaml

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

versions:

1.4.0-0,  1.2.0-0,  1.0.0-1,  1.0.0-0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-s4vectors:

>=0.40.2,<0.41.0a0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-analogue:

depends r-base:

>=4.3,<4.4.0a0

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:

requirements:

Installation

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 quay.io/biocontainers/bioconductor-fusesom:<tag>

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

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-fusesom/README.html)