recipe bioconductor-netsam

Network Seriation And Modularization






The NetSAM (Network Seriation and Modularization) package takes an edge-list representation of a weighted or unweighted network as an input, performs network seriation and modularization analysis, and generates as files that can be used as an input for the one-dimensional network visualization tool NetGestalt ( or other network analysis. The NetSAM package can also generate correlation network (e.g. co-expression network) based on the input matrix data, perform seriation and modularization analysis for the correlation network and calculate the associations between the sample features and modules or identify the associated GO terms for the modules.

package bioconductor-netsam

(downloads) docker_bioconductor-netsam



depends bioconductor-annotationdbi:


depends bioconductor-biomart:


depends bioconductor-go.db:


depends r-base:


depends r-dbi:


depends r-doparallel:


depends r-foreach:


depends r-igraph:


depends r-r2html:


depends r-seriation:


depends r-survival:


depends r-wgcna:




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-netsam

and update with::

   mamba update bioconductor-netsam

To create a new environment, run:

mamba create --name myenvname bioconductor-netsam

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

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