aracne.networks
This is the development version of aracne.networks; for the stable release version, see aracne.networks.
ARACNe-inferred gene networks from TCGA tumor datasets
Bioconductor version: Development (3.24)
This package provides access to ARACNe-inferred gene regulatory networks (regulons) from TCGA tumor datasets. The networks are hosted on Zenodo, downloaded on demand and cached locally with BiocFileCache. The package also contains a function to export them into plain-text format.
Author: Federico M. Giorgi [aut, cre]
, Mariano J. Alvarez [aut]
Maintainer: Federico M. Giorgi <federico.giorgi at gmail.com>
citation("aracne.networks")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("aracne.networks")
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("aracne.networks")| Using aracne.networks | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CancerData, ExperimentData, Genome, Homo_sapiens_Data |
| Version | 1.39.1 |
| License | file LICENSE |
| Depends | R (>= 4.0), viper |
| Imports | BiocFileCache, tools, utils |
| System Requirements | |
| URL | https://github.com/federicogiorgi/aracne.networks |
| Bug Reports | https://github.com/federicogiorgi/aracne.networks/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat |
| 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 | aracne.networks_1.39.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/aracne.networks |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/aracne.networks |
| Package Short Url | https://bioconductor.org/packages/aracne.networks/ |
| Package Downloads Report | Download Stats |