diffuStats

DOI: 10.18129/B9.bioc.diffuStats  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see diffuStats.

Diffusion scores on biological networks

Bioconductor version: 3.17

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>

Citation (from within R, enter citation("diffuStats")):

Installation

To install this package, start R (version "4.3") 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 1.20.0
In Bioconductor since BioC 3.6 (R-3.4) (6 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
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_1.20.0.tar.gz
Windows Binary diffuStats_1.20.0.zip
macOS Binary (x86_64) diffuStats_1.20.0.tgz
macOS Binary (arm64) diffuStats_1.20.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: