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.

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

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

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

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.

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