metabolic-pathways

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

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

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

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.

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

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.

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

prepBioCyc: Preprocess BioCyc files

PathVisio plugin to find relevant metabolic reactions from Rhea

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

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

MNXref: Reconciliation of metabolites and biochemical reactions for metabolic networks

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