Metab

Metab is an R package addressing the challenges associated with data processing in metabolomics, explicitly focusing on datasets generated by the Automated Mass Spectral Deconvolution and Identification System (AMDIS). While AMDIS is widely used in metabolomics, its datasets often require extensive manual correction, filtering, and reshaping to create reliable data for downstream analysis. These manual processes are laborious, time-consuming, and prone to human error, introducing additional technical variability to the data.
The Metab R package is an automated pipeline for analyzing metabolomics gas chromatography-mass spectrometry (GC-MS) datasets processed by AMDIS. By automating the data curation pipeline, Metab aims to streamline the workflow, eliminate manual errors, and enhance the efficiency of downstream analysis.

Topic

Metabolomics;Systems biology;Molecular interactions, pathways and networks

Detail

  • Operation: Formatting;Statistical calculation

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: GNU General Public License, version 2

  • Cost: Free

  • Version name: 1.36.0

  • Credit: The Health Research Council of New Zealand (HRC); Foundation for Research, Science and Technology (FRST).

  • Input: -

  • Output: -

  • Contact: Raphael Aggio ragg005@aucklanduni.ac.nz

  • Collection: -

  • Maturity: Stable

Publications

  • Metab: an R package for high-throughput analysis of metabolomics data generated by GC-MS.
  • Aggio R, et al. Metab: an R package for high-throughput analysis of metabolomics data generated by GC-MS. Metab: an R package for high-throughput analysis of metabolomics data generated by GC-MS. 2011; 27:2316-8. doi: 10.1093/bioinformatics/btr379
  • https://doi.org/10.1093/bioinformatics/btr379
  • PMID: 21697128
  • PMC: -

Download and documentation

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