Protein Graph Library

Single-cell Transcriptome and Regulome Analysis Pipeline

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

Deciphering driver regulators of cell fate decisions from single-cell RNA-seq data

A R/MATLAB package to construct and compare gene regulatory networks from single-cell transcriptomic data

TIMEOR: Trajectory Inference and Mechanism Exploration with Omics Data in R

Simulation and inference of gene regulatory networks based on transcriptional bursting

Source code for the paper "Fast and Accurate Inference of Gene Regulatory Networks through Robust Precision Matrix Estimation", by Passemiers et al.

Depicting pseudotime-lagged causality for accurate gene-regulatory inference

A Nextflow pipeline demonstrating how to train graph neural networks for gene regulatory network reconstruction using DREAM5 data.

A tool for gene regulatory inference

Simulation and inference of gene regulatory networks based on transcriptional bursting

Gene regulatory network reconstruction using random forest regression from only gene expression data from Single Cell RNA Seq Data. This project consisted of feature importance extraction and exploring different methods to investigate different and unique ways to extract feature importance to construct a gene regulatory network.

Gene Regulatory Interaction Network Simulator - GRiNS

The app visualizes a 3D graph of gene regulatory networks, allowing users to select a transcription factor and explore its neighboring interactions.

An explainable inductive learning model on gene regulatory and toxicogenomic knowledge graph (under development...)

Automated analysis tool for mutations in promoters, transcription factor binding sites, coding regions and protein domains in the context of gene regulatory networks.

Supplemental material associated with ALife 2020 conference submission.