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
Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations
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
Gold standard gene regulatory network data from the DREAM5 challenge.
Can Cells Talk?
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.
Construction of Gene Expression Network across 3 brain regions in the presence of Ethanol using WGCNA in R
pyEnGNet: optimized reconstruction of gene co-expression networks using multi-GPU
Fast Inference of Biological Networks from Directed Regulations (Findr) in Julia
Retinitis Pigmentosa gene interaction network website.
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.
Network-based analysis of omics with multi-objective optimization
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