Toolkit for Modelling and Simulation of Gene Expressions and Metabolism
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
scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.
🤝 Tool for mining KEGG pathways completeness data from eggNOG-mapper annotations
leADS: improved metabolic pathway inference based on active dataset subsampling
Metabolic pathway inference using non-negative matrix factorization with community detection
PathVisio plugin to find relevant metabolic reactions from Rhea
Pipeline plugins for PALADIN, providing HPC support, abundance (taxonomy, go terms), customized reports, etc
Diversity-based enumeration of optimal context-specific metabolic networks
CHAP: Modeling Metabolic Pathways as Groups (with Augmentation)
Serves as the backend code for https://www.curatemetabolicpathways.com
prepBioCyc: Preprocess BioCyc files
CaMP - cancer metabolic pathway viewer
reMap: relabeling metabolic pathway data with groups to improve prediction outcomes
Library to perform metabolic engineering tasks
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.
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