diffuStats

Diffusion scores on biological networks


Bioconductor version: Release (3.19)

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 "4.4") 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")
Case study: predicting protein function PDF R Script
Quick start HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, Genetics, GenomeWideAssociation, GraphAndNetwork, Metabolomics, Network, Normalization, Proteomics, Software, Transcriptomics
Version 1.24.0
In Bioconductor since BioC 3.6 (R-3.4) (7 years)
License GPL-3
Depends R (>= 3.4)
Imports grDevices, stats, methods, Matrix, MASS, checkmate, expm, igraph, Rcpp, RcppArmadillo, RcppParallel, plyr, precrec
System Requirements GNU make
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Suggests testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata, BiocStyle, reshape2, utils
Linking To Rcpp, RcppArmadillo, RcppParallel
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Package Archives

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

Source Package diffuStats_1.24.0.tar.gz
Windows Binary diffuStats_1.24.0.zip (64-bit only)
macOS Binary (x86_64) diffuStats_1.24.0.tgz
macOS Binary (arm64) diffuStats_1.24.0.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/
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