Explore biomolecular pathways in Reactome from the command-line or a Python script

A network based gene classification library to generate genome wide predictions about genes that are functionally similar to the input gene list.

MGN-Net: A novel Graph Neural Network for integrating heterogenous graph population derived from multiple sources.

MCRM: Mother Compact Recurrent Memory

Prospecting Optimal Pathways with PYthon: Tools for creating and exploring metabolic reaction networks.

The BioNE is a new pipeline that integrates embedding results from different graph embedding methods, providing a more comprehensive knowledge of the network and therefore better performance on prediction tasks.

Converting KGML encoded KEGG pathways to the SIF file format

Converting SBGN encoded pathways to the SIF file format

Converting SBGN-encoded pathways to the SIF file format

A python data science library to build and analyze biological networks from spatial transcriptomics data. Allows inclusion of spatial information into the networks, going a step beyond graphs derived from scRNA-seq techniques.

This repository provides classic clustering algorithms and various internal cluster quality validation metrics and also visualization capabilities to analyse the clustering results

Repositório para apresentação de código desenvolvido pelo grupo 2 para a UC Algoritmos Avançados para a Bioinformática do Mestrado em Bioinformática, ano lectivo 23-24.

Webinar: Large-scale Biological Network Analysis and Visualization Using CyVerse

Pathway Activity Analysis and Metabolite Annotation for Untargeted Metabolomics using Probabilistic Modeling

Dockerized BIONIC

Translation of the MOGAMUN algorithm in Python as part of a biological network modeling course.

Multi-omics differential dependency network inference

This is the backend service repository that makes Drugst.One work. Drugst.One is a plug-and-play solution to make your biomedical (web-)tool drug repurposing ready. With just three lines of code the plugin can be integrated into your website within a few minues of work.