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

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

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

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

Identifying reprogrammed metabolic routes given omics data.

Library to perform metabolic engineering tasks

scCellFie offers advanced analysis of metabolic functions from single-cell and spatial transcriptomics. Efficient and user-friendly, it runs on Python and integrates with Scanpy, enabling single-cell and spatial analysis of metabolic tasks.

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

🤝 Tool for generating KEGG pathways completeness heatmaps from eggNOG-mapper annotations

prepBioCyc: Preprocess BioCyc files

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

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

A basic network of human metabolism, including key enzymes, intermediates, and hormonal influences

MNXref: Reconciliation of metabolites and biochemical reactions for metabolic networks

PathVisio plugin to find relevant metabolic reactions from Rhea

Serves as the backend code for https://www.curatemetabolicpathways.com

leADS: improved metabolic pathway inference based on active dataset subsampling