CoreMS is a comprehensive mass spectrometry software framework

Galaxy tools for metabolomics maintained by Workflow4Metabolomics

Metabolome Annotation Workflow

MetMiner: A user-friendly pipeline for large-scale plant metabolomics data analysis

A Python package for metabolite enrichment analysis.

R package that provide interactive graphical interface for metabolic profiling

Composite Spectra Analysis

MS_targeted is an open-source command-line pipeline for statistical analysis of mass spectrometry metabolomics data.

Package for automation of statistics that are widely used in metabolomics.

MetaboDynamics: a framework of probabilistic models to analyze longitudinal metabolomics data

GitHub repository for MetCirc. The development version in Bioconductor can be found at:

Differential analysis of targeted Isotope-labeled Metabolomics data

GitHub repository for MetNet. The development version in Bioconductor can be found at:

RTMet is a data workflow to process FIA-MS data coming from a bioreactor, find metabolites and fluxes, and send a feedback command to the system.

R package for the estimation of metabolome-wide significance level and corresponding effective number of tests

Role of genomics on regulating rice grain metabolic variability under warmer nights: A statistical and image-based deep learning approach

The lingress project is to develop the pipeline to analyse the Nuclear magnetic resonance (NMR) dataset using a univariate linear regression model. This package contains the analysis with linear regression (OLS) and visualises the interpretation of the results with a p-value of all NMR peaks.

Easily install, load and update R packages for high-resolution metabolomics analyses

MTXQCvX2 fluffy adventure is a quality and data processing tool for GC-MS based metabolomics experiments.