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

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

Scalable Tool for Gene Network Reverse Engineering

Finite State Projection algorithms for chemical reaction networks

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

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

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

Network-guided matrix completion

Genome Network Ala Neural Network

Intuitive Nonparametric Gene Network Search Algorithm

Arabidopsis Thaliana TRanscriptionAl Circadian neTwORk, a web based tool developed using the R package shiny for the exploration and analysis of a transcriptional network in Arabidopsis thaliana constituted by circadian and light responsive transcriptional factors and regulators

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.

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

Gold standard gene regulatory network data from the DREAM5 challenge.

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

Retinitis Pigmentosa gene interaction network website.

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.