Network-Oriented Repurposing of Drugs Python Package

Network Regression Embeddings reveal cell-type Transcription Factor coordination for target gene (TG) regulation

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

Links to interesting courses, tutorials, papers, software etc. related to single-cell omics data analysis

Latex scripts to compile my PhD thesis

Gold standard gene regulatory network data from the DREAM5 challenge.

Prokaryote Gene Regulatory Network (ProGRN) Inference Pipeline

A Lightning-fast algorithm for Gene Regulatory Network inference from gene expression data

Python implementation of the PCA-CMI algorithm proposed by Zhang et al. and comparison of the results with the IC algorithm to predict gene regulatory network skeleton and edge orientations.

Training materials for the bioinformatic approaches used in my MSc thesis.

GRADIS_eX project extended GRADIS (a supervised learning of Gene Regulatory Network inference) by incorporating transcription factor binding motifs on promoter regions on the DNA.

TENET refined