Toolkit for Modelling and Simulation of Gene Expressions and Metabolism

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

🤝 Tool for mining KEGG pathways completeness data from eggNOG-mapper annotations

Knowledge graph construction for pharmacogenomic data integration. Semantic modeling of drug-gene interactions, metabolic pathways, and clinical phenotypes using graph databases and ontology frameworks for precision medicine applications.

scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.

This repository collects my project for the Applied Genomics course. It includes the presentation on the chromosome-scale reference genome of the Alpine marmot, integrating multi-omics to study hibernation and high-altitude adaptation. Teaching materials (notes, transcripts, slides) used during the course are also provided for study purposes.

CaMP - cancer metabolic pathway viewer

MNXref: Reconciliation of metabolites and biochemical reactions for metabolic networks

Code and data repository for Modeling Metabolic Fluxes Using Deep Learning Based on Enzyme Variations

A tool for representing genomic potential and transcriptomic expression into KEGG pathways

Library to perform metabolic engineering tasks

Pipeline plugins for PALADIN, providing HPC support, abundance (taxonomy, go terms), customized reports, etc

Infer metabolic directions from moment differences of mass-weighted intensity distributions

Go REST API to replace Genbank, Uniprot, Rhea, and CHEMBL

Ⓜ️ Metabolic network completion

Identifying reprogrammed metabolic routes given omics data.

prepBioCyc: Preprocess BioCyc files

leADS: improved metabolic pathway inference based on active dataset subsampling

CHAP: Modeling Metabolic Pathways as Groups (with Augmentation)