diffuStats

DOI: 10.18129/B9.bioc.diffuStats    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see diffuStats.

Diffusion scores on biological networks

Bioconductor version: 3.9

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 and benchmarking.

Author: Sergio Picart-Armada and Alexandre Perera-Lluna

Maintainer: Sergio Picart-Armada <sergi.picart at upc.edu>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("diffuStats")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("diffuStats")

 

PDF	R Script	Case study: predicting protein function
HTML	R Script	Quick start
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, GraphAndNetwork, Network, Software
Version	1.4.0
In Bioconductor since	BioC 3.6 (R-3.4) (2 years)
License	GPL-3
Depends	R (>= 3.4)
Imports	grDevices, stats, methods, Matrix, MASS, expm, igraph, Rcpp, RcppArmadillo, RcppParallel, plyr, precrec
LinkingTo	Rcpp, RcppArmadillo, RcppParallel
Suggests	testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata, BiocStyle, reshape2
SystemRequirements	GNU make
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	diffuStats_1.4.0.tar.gz
Windows Binary	diffuStats_1.4.0.zip
Mac OS X 10.11 (El Capitan)	diffuStats_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/diffuStats
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/diffuStats
Package Short Url	https://bioconductor.org/packages/diffuStats/
Package Downloads Report	Download Stats