Scalable Tool for Gene Network Reverse Engineering

Finite State Projection algorithms for chemical reaction networks

Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations

DelaySSAToolkit.jl: a tool in Julia for stochastic simulation with delays

Text mining tool to retrieve protein-protein interactions from the scientific literature.

Intuitive Nonparametric Gene Network Search Algorithm

A computational method to rank and infer drug-responsive cell population towards in-silico drug perturbation using a target-perturbed gene regulatory network (tpGRN) for single-cell transcriptomic data

Retinitis Pigmentosa gene interaction network website.

Network-guided matrix completion

A web based app developed using the R package shiny to explore the transcriptional network downstream from the Arabidopsis thaliana transcriptional factor BRC1.

Construction of Gene Expression Network across 3 brain regions in the presence of Ethanol using WGCNA in R

Network-based analysis of omics with multi-objective optimization

R package to predict gene feed forward loops using mediation analysis. Analyses integrate observed miRNA and mRNA expression data and database information on gene interactions.

Gold standard gene regulatory network data from the DREAM5 challenge.

Can Cells Talk?

pyEnGNet: optimized reconstruction of gene co-expression networks using multi-GPU

This repo offers a workflow dedicated to utilizing BERTopic for Semantic Graph-based information retrieval in nutrigenomics. It includes Jupyter notebooks on topic modeling and semantic graph creation, aimed at enhance genetic literature exploration. Ideal for genomic researchers, it simplifies the analysis of nutrition-related genetic information.

Genome Network Ala Neural Network

The CyEnGNet-App is a plugin for Cytoscape. It implements the EnGNet algorithm, a powerful network analysis method. This app allows users to directly generate the output network in Cytoscape.

Fast Inference of Biological Networks from Directed Regulations (Findr) in Julia