Bioconductor - diffuStats
Bioconductor 3.22
Software Packages
diffuStats
diffuStats
This is the
released
version of diffuStats; for the devel version, see
diffuStats
Diffusion scores on biological networks
DOI:
10.18129/B9.bioc.diffuStats
Bioconductor version:
Release (3.22)
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
Citation (from within R, enter
citation("diffuStats")
):
Installation
To install this package, start R (version "4.5") 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
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Reference Manual
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Details
biocViews
GeneExpression
Genetics
GenomeWideAssociation
GraphAndNetwork
Metabolomics
Network
Normalization
Proteomics
Software
Transcriptomics
Version
1.30.0
In Bioconductor since
BioC 3.6 (R-3.4) (8.5 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
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Installation
instructions to use this package in your R session.
Source Package
diffuStats_1.30.0.tar.gz
Windows Binary (x86_64)
diffuStats_1.30.0.zip
(64-bit only)
macOS Binary (x86_64)
diffuStats_1.30.0.tgz
macOS Binary (arm64)
diffuStats_1.30.0.tgz
Source Repository
git clone https://git.bioconductor.org/packages/diffuStats
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/diffuStats
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