BioNAR
This is the development version of BioNAR; for the stable release version, see BioNAR.
Biological Network Analysis in R
Bioconductor version: Development (3.21)
the R package BioNAR, developed to step by step analysis of PPI network. The aim is to quantify and rank each protein’s simultaneous impact into multiple complexes based on network topology and clustering. Package also enables estimating of co-occurrence of diseases across the network and specific clusters pointing towards shared/common mechanisms.
Author: Colin Mclean [aut], Anatoly Sorokin [aut, cre], Oksana Sorokina [aut], J. Douglas Armstrong [aut, fnd], T. Ian Simpson [ctb, fnd]
Maintainer: Anatoly Sorokin <lptolik at gmail.com>
citation("BioNAR")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("BioNAR")
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("BioNAR")| BioNAR: Biological Network Analysis in R | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GraphAndNetwork, Network, Software |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0), igraph (>= 2.0.1.1), poweRlaw, latex2exp, RSpectra, Rdpack |
| Imports | stringr, viridis, clusterCons, fgsea, grid, methods, AnnotationDbi, dplyr, GO.db, org.Hs.eg.db(>= 3.19.1), rSpectral, WGCNA, ggplot2, ggrepel, minpack.lm, cowplot, data.table, scales, stats, Matrix |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/lptolik/BioNAR/issues/ |
See More
| Suggests | knitr, BiocStyle, magick, rmarkdown, igraphdata, testthat (>= 3.0.0), vdiffr, devtools, pander, plotly, randomcoloR |
| Linking To | |
| 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 | BioNAR_1.9.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/BioNAR |
| Source Repository (Developer Access) | git clone [email protected]:packages/BioNAR |
| Bioc Package Browser | https://code.bioconductor.org/browse/BioNAR/ |
| Package Short Url | https://bioconductor.org/packages/BioNAR/ |
| Package Downloads Report | Download Stats |