README.md

In ingres: Infer Gene Probabilistic Boolean Networks from Single-Cell Data

ingres

I*nferring Probabilistic Boolean Networks of Gene Regulation Using Protein Activity Enrichment S*cores

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).

ingres documentation built on Sept. 14, 2022, 9:05 a.m.