- recipe bioconductor-diffustats
Diffusion scores on biological networks
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/diffuStats.html
- License:
GPL-3
- Recipe:
- 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)