metabolomics

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The codebase of the OpenMS project

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

Python library for processing (tandem) mass spectrometry data and for computing spectral similarities.

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

LC-MS data processing tool for large-scale metabolomics experiments.

A deep learning toolkit for mass spectrometry

Data toolkits for processing NMR, MALDI MSI, MALDI single cell, Raman Spectroscopy, LC-MS and GC-MS raw data, chemoinformatics data analysis and data visualization.

CoreMS is a comprehensive mass spectrometry software framework

Public Workflows at GNPS

A Python 3 implementation of orthogonal projection to latent structures

In silico chemical library engine for high-accuracy chemical property prediction

TidyMS: Tools for working with MS data in untargeted metabolomics

Cloud engine and platform for metabolite annotation for imaging mass spectrometry

sirius-libs - Metabolomics mass spectrometry framework for molecular formula identification of small molecules written in Java

Parsers for chromatography data in R (HPLC-DAD/UV, GC-FID, MS)

Compare different differential abundance and expression methods

Meet FIORA! An in silico fragmentation algorithm designed to predict tandem mass spectra (MS/MS) with high accuracy. Using graph neural networks, FIORA models bond cleavages, fragment intensities, and estimates retention times (RT) and collision cross sections (CCS).

National Microbiome Data Collaborative (NMDC) unified data model