recipe bioconductor-diffustats

Diffusion scores on biological networks

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-diffustats/meta.yaml

Links:

biotools: diffuStats, doi: 10.1093/bioinformatics/btx632

Label propagation approaches are a widely used procedure in computational biology for giving context to molecular entities using network data. Node labels, which can derive from gene expression, genome-wide association studies, protein domains or metabolomics profiling, are propagated to their neighbours in the network, effectively smoothing the scores through prior annotated knowledge and prioritising novel candidates. The R package diffuStats contains a collection of diffusion kernels and scoring approaches that facilitates their computation, characterisation and benchmarking.

package bioconductor-diffustats

versions:

1.22.0-0,  1.20.0-0,  1.18.0-2,  1.18.0-1,  1.18.0-0,  1.14.0-2,  1.14.0-1,  1.14.0-0,  1.12.0-0, 

1.22.0-0,  1.20.0-0,  1.18.0-2,  1.18.0-1,  1.18.0-0,  1.14.0-2,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.2-0,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  0.104.0-0,  0.102.0-0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-checkmate:

depends r-expm:

depends r-igraph:

depends r-mass:

depends r-matrix:

depends r-plyr:

depends r-precrec:

depends r-rcpp:

depends r-rcpparmadillo:

depends r-rcppparallel:

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-diffustats

and update with::

   mamba update bioconductor-diffustats

To create a new environment, run:

mamba create --name myenvname bioconductor-diffustats

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-diffustats:<tag>

(see `bioconductor-diffustats/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-diffustats/README.html)