metabolic-pathways

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

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

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

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

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

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

Toolkit for Modelling and Simulation of Gene Expressions and Metabolism

Ⓜ️ Metabolic network completion

Diversity-based enumeration of optimal context-specific metabolic networks

Library to perform metabolic engineering tasks

Identifying reprogrammed metabolic routes given omics data.

A robust and scalable framework for resource-constraint models through stochastic tuning of deep learning-predicted kinetic parameters

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

reMap: relabeling metabolic pathway data with groups to improve prediction outcomes

prepBioCyc: Preprocess BioCyc files

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.

Metabolic pathway inference using non-negative matrix factorization with community detection

PathVisio plugin to find relevant metabolic reactions from Rhea

A pathway-level bioinformatics tool for conservative evidence-based detection of bioremediation capabilities from bacterial genome annotations.