Inferring Probabilistic Boolean Networks of Gene Regulation Using Protein Activity Enrichment Scores
Given a gene regulatory boolean network and a RNA-seq dataset, ingres computes protein activity normalised enrichment scores using VIPER, and then produces a probabilistic network using the scores as probabilities for fixed node activation or deactivation, in addition to the original boolean functions.
Installation
You can install the development version of ingres with:
# install.packages("devtools")
devtools::install_github("CBigOxf/ingres")You may need to manually install some of the BioConductor dependencies before you can install ingres:
# install.packages("BiocManager")
BiocManager::install(c("viper", "AnnotationDbi", "org.Hs.eg.db", "aracne.networks"))Citation
To cite ingres in publications use:
Victori, P. & Buffa, F. M. Ingres: from single-cell RNA-seq data to single-cell probabilistic Boolean networks. 2022.09.04.506528 Preprint at https://doi.org/10.1101/2022.09.04.506528 (2022).