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diffuStats

This is the development version of diffuStats; for the stable release version, see diffuStats.

Diffusion scores on biological networks


Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.23.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 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
URL
See More
Suggests testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata, BiocStyle, reshape2, utils
Linking To Rcpp, RcppArmadillo, RcppParallel
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
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Package Archives

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

Source Package diffuStats_1.23.0.tar.gz
Windows Binary diffuStats_1.23.0.zip
macOS Binary (x86_64) diffuStats_1.23.0.tgz
macOS Binary (arm64) diffuStats_1.23.0.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