recipe bioconductor-birewire

High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals)

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-birewire/meta.yaml

Links:

biotools: birewire

Fast functions for bipartite network rewiring through N consecutive switching steps (See References) and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. Includes functions for the analysis of the introduced randomness across the switching steps and several other routines to analyse the resulting networks and their natural projections. Extension to undirected networks and directed signed networks is also provided. Starting from version 1.9.7 a more precise bound (especially for small network) has been implemented. Starting from version 2.2.0 the analysis routine is more complete and a visual montioring of the underlying Markov Chain has been implemented. Starting from 3.6.0 the library can handle also matrices with NA (not for the directed signed graphs). Since version 3.27.1 it is possible to add a constraint for dsg generation: usually positive and negative arc between two nodes could be not accepted.

package bioconductor-birewire

(downloads) docker_bioconductor-birewire

versions:
3.34.0-0,  3.32.0-0,  3.30.0-2,  3.30.0-1,  3.30.0-0,  3.26.5-0,  3.26.2-0,  3.26.0-0,  3.24.0-0, 

3.34.0-0,  3.32.0-0,  3.30.0-2,  3.30.0-1,  3.30.0-0,  3.26.5-0,  3.26.2-0,  3.26.0-0,  3.24.0-0,  3.22.0-1,  3.22.0-0,  3.20.0-0,  3.18.0-0,  3.16.0-1,  3.16.0-0,  3.14.0-0,  3.12.0-0,  3.10.0-0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.3,<4.4.0a0

depends r-igraph:

depends r-matrix:

depends r-rtsne:

depends r-slam:

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-birewire

and update with::

   mamba update bioconductor-birewire

To create a new environment, run:

mamba create --name myenvname bioconductor-birewire

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-birewire:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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