diffuStats
This is the released version of diffuStats; for the devel version, see diffuStats.
Diffusion scores on biological networks
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.32.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 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_1.32.0.tar.gz |
| Windows Binary (x86_64) | diffuStats_1.32.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | diffuStats_1.32.0.tgz |
| macOS Binary (sonoma-arm64) | diffuStats_1.32.0.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 |