ARACNe-inferred gene regulatory networks (regulons) from TCGA tumor datasets, distributed through Bioconductor.
The 25 networks are hosted on Zenodo (doi:10.5281/zenodo.22918956), downloaded on demand and cached locally with BiocFileCache.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("aracne.networks")
library(aracne.networks)
# available networks
listRegulons()
# download (first time only) and load the Bladder Carcinoma network
regulonblca <- getRegulon("blca")
# export it as a text table
write.regulon(regulonblca, file = "blca_network.txt")
Since version 1.39.1 the networks are no longer bundled in the package:
replace data(regulonblca) with regulonblca <- getRegulon("blca").
The package code is distributed under the terms in LICENSE. The network
files on Zenodo are released under
CC BY-NC-ND 4.0:
commercial use is not permitted.
Giorgi, F.M. et al. (2016) ARACNe-AP: Gene Network Reverse Engineering through Adaptive Partitioning inference of Mutual Information. Bioinformatics 32(14):2233-2235. doi:10.1093/bioinformatics/btw216
Alvarez, M.J. et al. (2016) Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Nature Genetics 48(8):838-847. doi:10.1038/ng.3593