Tools: Overview

Load and analyze your own database

Analyse NIH Metabolomics Data Repository studies

MS Searches

  • MS Searches: Precursor ion searches on metabolite and lipid databases in single or batch mode.

REST Service

  • REST Service: The Metabolomics WorkBench REST service enables access to a variety of data (including metabolite structures, study metadata and experimental results) using HTTP requests.

Web tools

  • MetaBatch Omic Browser: A web application developed at MD Anderson Cancer Center (John Weinstein group) for analysis and visualization of batch effects in NMDR datasets. Included are dynamically interactive Next-Generation Clustered Heat Maps, PCA+, UMAP, box plot, violin plot, and other visualizations for essentially all NMDR datasets.
  • Next-Generation Clustered Heat Map (NGCHM) Viewer: A dynamically interactive web environment, developed at MD Anderson Cancer Center (John Weinstein group), for exploration of omic datasets with extreme zooming, panning, searches, covariate bars, dozens of link-outs, high-resolution graphics, and other features. Included is coordination with UMAP, t-SNE, PCA+, pathway, and other visualizations, with quantitative analyses. Updates are done periodically as additional datasets are added to NMDR. https://www.biorxiv.org/content/10.1101/2020.10.31.363580v1.full.pdf.

Docker tools

  • MSCAT: A dockerized application developed by the group led by Katerina Kechris and Debashis Ghosh at the University of Colorado Anschutz Medical Campus in conjunction with the Metabolomics Workbench. The application provides a database of metabolomics software tools and allows one to generate potential software workflows using an online interface.
  • PaIRKAT: A dockerized application developed by the group led by Katerina Kechris and Debashis Ghosh at the University of Colorado Anschutz Medical Campus. PaIRKAT is a pathway integrated tool for improving testing power on high dimensional data by including graph topography in the kernel machine regression setting.

Shiny apps

  • RefMet name search: A Shiny app developed by the Metabolomics Workbench to search the RefMet standardized metabolite nomenclature database by metabolite name.
  • RefMet MS search: A Shiny app developed by the Metabolomics Workbench to search the RefMet standardized metabolite nomenclature database with a list of m/z values (Input is a text file with a single column of m/z values).
  • MetStat search: A Shiny app developed by the Metabolomics Workbench to display summary information in NMDR based on analysis method, species, sample source and disease association.
  • Marr: A Shiny app developed by the group led by Katerina Kechris and Debashis Ghosh at the University of Colorado Anschutz Medical Campus which implements the method Maximum Rank Reproducibility (MaRR), a nonparametric approach that detects reproducible signals using a maximal rank statistic for high-dimensional biological data. An R package version is also available for download from Github.

External Tools

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