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ingres

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).

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Version

Install

install.packages('ingres')

Version

1.0.0

License

GPL (>= 3)

Issues

1

Pull Requests

0

Stars

3

Forks

1

Maintainer

Pedro Victori

Last Published

September 14th, 2022

Functions in ingres (1.0.0)

produceNetworkForCluster

Produce a tidygraph network for a given cluster
network

An example network, in the format required by the package. The network is a modified version of the one in Remy et al. Cancer Res 75, 4042–4052 (2015)
small_blca_wang

An example small Seurat object, using dataset GSE130001 from Wang et al. Genome Med. 2020 Dec;12(1):24.
ingres-class

The ingres class.
ingres-package

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

Pipe operator
network_genes

An example dataframe with the genes contained in the network, in the format required by the package
performViper

Perform VIPER
produceNetworkForCell

Produce a tidygraph network for a given cell
viper_results

The results of running performViper() on an ingres object created with small_blca_wang, intended to speed up vignettes and examples. This data frame was subset to only contain the genes in the network_genes file, so to keep the file size small.
cellGenesHeatmap

Plot a cell heatmap
graphmlAsTidy

Convert GraphML format to tidygraph
computePbnByCluster

Compute a Probabilistic Boolean Network (PBN) for each cluster or each cell
ginmlToGraphml

Convert a GinSim file into a GraphML file GinSim files have the extension .zginml. This utility function converts such files into the GraphML format. keeping the kind - fate, input or gene -, the edge sign and the rule - formulae - data.
createIngresObject

Create a new ingres object.
cellPbnPlot

Plot a cell PBN
clusterGenesHeatmap

Plot a cluster heatmap
clusterPbnPlot

Plot a cluster PBN
plotSelectedCell

Plot the PBN of a cell selected in an interactive plot.
printAllNodes

Print all nodes in a network For testing and checks purposes.
createIngresObjectFromSeurat

Create a new ingres object using the expression data in a Seurat object.
produceBoolnetNetwork

Convert an ingres network into a BoolNet one
createNetworkGenesTemplate

Create a network genes data frame. Optionally store it as csv and open it for editing To create an ingres object, a data frame with the network nodes and the corresponding gene symbols must be provided. This function simplifies the process. If the gene nodes are correct gene symbols, then modification is not needed and the returned data frame can be directly passed to the ingres constructors.