recipe bioconductor-mosbi

Molecular Signature identification using Biclustering

Homepage:

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

License:

AGPL-3 + file LICENSE

Recipe:

/bioconductor-mosbi/meta.yaml

This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters on molecular omics data. This is done by computing similarity networks of biclusters and filtering for overlaps using a custom error model. After that, the louvain modularity it used to extract bicluster communities from the similarity network, which can then be converted to ensemble biclusters. Additionally, MoSBi includes several network visualization methods to give an intuitive and scalable overview of the results. MoSBi comes with several biclustering algorithms, but can be easily extended to new biclustering algorithms.

package bioconductor-mosbi

versions:

1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.0.3-1,  1.0.3-0,  1.0.0-0

depends bioconductor-fabia:

>=2.48.0,<2.49.0

depends bioconductor-fabia:

>=2.48.0,<2.49.0a0

depends bioconductor-qubic:

>=1.30.0,<1.31.0

depends bioconductor-qubic:

>=1.30.0,<1.31.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-akmbiclust:

depends r-base:

>=4.3,<4.4.0a0

depends r-bh:

depends r-biclust:

depends r-igraph:

depends r-isa2:

depends r-rcolorbrewer:

depends r-rcpp:

depends r-rcppparallel:

depends r-xml2:

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-mosbi

and update with::

   mamba update bioconductor-mosbi

To create a new environment, run:

mamba create --name myenvname bioconductor-mosbi

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-mosbi:<tag>

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

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Link to this page

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