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("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 | R Script | |
| Quick start | HTML | R Script |
| Reference Manual | ||
| 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 |
| 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 | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | diffuStats_1.24.0.tar.gz |
| Windows Binary (x86_64) | 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/ |
| Package Downloads Report | Download Stats |