diffuStats

DOI: 10.18129/B9.bioc.diffuStats  

Diffusion scores on biological networks

Bioconductor version: Release (3.16)

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.

Author: Sergio Picart-Armada [aut, cre], Alexandre Perera-Lluna [aut]

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

Installation

To install this package, start R (version "4.2") and enter:

if (!require("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, Genetics, GenomeWideAssociation, GraphAndNetwork, Metabolomics, Network, Normalization, Proteomics, Software, Transcriptomics
Version	1.18.0
In Bioconductor since	BioC 3.6 (R-3.4) (5.5 years)
License	GPL-3
Depends	R (>= 3.4)
Imports	grDevices, stats, methods, Matrix, MASS, checkmate, expm, igraph, Rcpp, RcppArmadillo, RcppParallel, plyr, precrec
LinkingTo	Rcpp, RcppArmadillo, RcppParallel
Suggests	testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata, BiocStyle, reshape2, utils
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_1.18.0.tar.gz
Windows Binary	diffuStats_1.18.0.zip (64-bit only)
macOS Binary (x86_64)	diffuStats_1.18.0.tgz
macOS Binary (arm64)	diffuStats_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/diffuStats
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/diffuStats
Bioc Package Browser	https://code.bioconductor.org/browse/diffuStats/
Package Short Url	https://bioconductor.org/packages/diffuStats/
Package Downloads Report	Download Stats