Awesome Metabolomics

A curated list of awesome Metabolomics frameworks, libraries, software, and resources.

Inspired by awesome-python.

Databases

• RaMP - A comprehensive database providing access to biological pathways, ontologies, chemical descriptions, and reactions. It draws from HMDB, KEGG, Reactome, and WikiPathways among others. Visit RaMP

• KEGG - The Kyoto Encyclopedia of Genes and Genomes offers a systematic analysis of gene functions, connecting genes to molecules in the network. It features extensive metabolic and regulatory pathways. Explore KEGG

• Reactome - An open-source, curated pathway database that supports the visualization, interpretation, and analysis of pathway knowledge. It includes a vast collection of human pathways and bioinformatic tools. Discover Reactome

• BioCyc - A collection of pathway/genome databases with quality data curated from thousands of publications. It offers tools for navigating, visualizing, and analyzing the databases. Browse BioCyc

• HMDB (Human Metabolome Database) - Contains detailed information about small molecule metabolites found in the human body, supporting metabolomics, clinical chemistry, and biomarker discovery. Check out HMDB

Tools and Software

• XCMS and MZmine: Comprehensive platforms for processing LC-MS data, offering feature detection, alignment, and quantification. Essential for in-depth metabolomics analysis.

• asari: A cutting-edge tool addressing mass alignment and feature selection issues, implementing the "mass track" concept for improved metabolite identification accuracy. Learn more about asari

• CSI:FingerID within SIRIUS: Facilitates compound identification by predicting molecular formulas and matching them against database entries, using mass spectrometry data. Explore CSI:FingerID

• MetaboAnalyst: A web-based platform for comprehensive metabolomics data analysis, including statistical analysis and pathway analysis. Visit MetaboAnalyst

Learning Resources

• Metabolomics Society - Offers a platform for education, resources, and networking within the metabolomics community. Visit Metabolomics Society

Community Forums

• Engage with experts and peers in the field through online forums and discussion groups dedicated to metabolomics research.

Remember to check each resource for the latest updates and tools available for your metabolomics research needs.