recipe bioconductor-opossom

Comprehensive analysis of transcriptome data

Homepage:

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

License:

GPL (>=2)

Recipe:

/bioconductor-opossom/meta.yaml

This package translates microarray expression data into metadata of reduced dimension. It provides various sample-centered and group-centered visualizations, sample similarity analyses and functional enrichment analyses. The underlying SOM algorithm combines feature clustering, multidimensional scaling and dimension reduction, along with strong visualization capabilities. It enables extraction and description of functional expression modules inherent in the data.

package bioconductor-opossom

versions:

2.20.0-0,  2.18.0-0,  2.16.0-1,  2.16.0-0,  2.12.0-2,  2.12.0-1,  2.12.0-0,  2.10.0-0,  2.8.0-1, 

2.20.0-0,  2.18.0-0,  2.16.0-1,  2.16.0-0,  2.12.0-2,  2.12.0-1,  2.12.0-0,  2.10.0-0,  2.8.0-1,  2.8.0-0,  2.6.0-0,  2.4.0-0,  2.2.0-1,  2.0.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0a0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-biomart:

>=2.58.0,<2.59.0a0

depends bioconductor-graph:

>=1.80.0,<1.81.0

depends bioconductor-graph:

>=1.80.0,<1.81.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-ape:

depends r-base:

>=4.3,<4.4.0a0

depends r-fastica:

depends r-fdrtool:

depends r-igraph:

>=1.0.0

depends r-pixmap:

depends r-png:

depends r-rcpp:

depends r-rcppparallel:

depends r-rcurl:

depends r-scatterplot3d:

depends r-tsne:

depends r-xml:

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-opossom

and update with::

   mamba update bioconductor-opossom

To create a new environment, run:

mamba create --name myenvname bioconductor-opossom

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-opossom:<tag>

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

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Link to this page

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