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

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

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

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

Toolkit for Modelling and Simulation of Gene Expressions and Metabolism

Ⓜ️ Metabolic network completion

Identifying reprogrammed metabolic routes given omics data.

Library to perform metabolic engineering tasks

Diversity-based enumeration of optimal context-specific metabolic networks

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

scCellFie, inspired by the MATLAB-based CellFie tool, offers advanced analysis of metabolic functions on Python using single-cell and spatial transcriptomics. Efficient and user-friendly, it integrates with Scanpy to extend CellFie's capabilities, enabling in-depth single-cell and spatial metabolic task analysis.

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

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

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

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

prepBioCyc: Preprocess BioCyc files

leADS: improved metabolic pathway inference based on active dataset subsampling

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