Metabolomics Data Analysis Tools
R Packages for Metabolomics Data Analysis
- MSnbase: R/Bioconductor package for handling and processing mass spectrometry and proteomics data.
- XCMS: Pre-processing high-resolution mass spectrometry data, including peak detection, alignment, and quantification.
- CAMERA: Companion to XCMS for annotation of isotopes and adducts in LC/MS data.
- MetaboAnalystR: Comprehensive metabolomics data analysis, including statistical analysis, data normalization, and visualization.
- MAI (Mechanism-aware Imputation): Imputes missing data in metabolomics using a two-step approach.
- MSPrep: Tools for the pre-analytic processing of MS-based metabolomics data.
- BATMAN: Bayesian automated metabolite analyzer for NMR spectra.
- MetaboDiff: Differential abundance analysis for metabolomics data.
- GlobalAncova: Functions for applying the global test in multivariate analysis of covariance, useful in metabolomics.
Python Packages for Metabolomics Data Analysis
- pyOpenMS: Python interface to the OpenMS library, enabling mass spectrometry data processing.
- mzML2ISA: Converts mzML files to ISA-Tab format for metabolomics experiments.
- nPYc-Toolbox: Toolbox for the analysis of large-scale NMR and mass spectrometry datasets.
- El-MAVEN: A fast, robust LC/MS data processing tool for untargeted and targeted analysis.
Tools for Metabolomics Data Analysis
- MetaboAnalyst: Web-based tool suite for comprehensive metabolomics data analysis.
- MZmine: Open-source software for mass-spectrometry data processing, focusing on LC-MS and GC-MS data.
- XCMS Online: A cloud-based platform for the processing of mass spectrometry data, including peak detection, alignment, and annotation.
- Galaxy-M: Workflow management platform for metabolomics, offering tools for data processing, analysis, and visualization.
- MetExplore: Web server for metabolic network exploration and pathway analysis.
- MetFrag: Tool for in-silico fragment generation and spectral match scoring, useful for metabolite identification.
File Converters for Metabolomics Data
- ThermoRawFileParser: A tool to convert Thermo Fisher Scientific RAW files into open formats such as mzML, mzXML, and MGF.
- ProteoWizard (msConvert): A widely used tool for converting raw mass spectrometry data files from various vendor formats to open formats such as mzML, mzXML, and MGF.
- mzML2ISA: Converts mzML files to ISA-Tab format.
- OpenMS FileConverter: Part of the OpenMS suite, this tool allows for the conversion of mass spectrometry data files between various formats.