diffuStats

DOI: 10.18129/B9.bioc.diffuStats    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see diffuStats.

Diffusion scores on biological networks

Bioconductor version: 3.10

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	1.6.0
In Bioconductor since	BioC 3.6 (R-3.4) (2.5 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
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	diffuStats_1.6.0.tar.gz
Windows Binary	diffuStats_1.6.0.zip
Mac OS X 10.11 (El Capitan)	diffuStats_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/diffuStats
Source Repository (Developer Access)	git clone [email protected]:packages/diffuStats
Package Short Url	https://bioconductor.org/packages/diffuStats/
Package Downloads Report	Download Stats