Metabolomics Python Packages

pyopenms

The codebase of the OpenMS project

matchms

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

nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

metbit

Metabolomics data analysis and visualization tools.

depthcharge-ms

A deep learning toolkit for mass spectrometry

msi-recal

Cloud engine and platform for metabolite annotation for imaging mass spectrometry

pyopls

A Python 3 implementation of orthogonal projection to latent structures

metaspace2020

Cloud engine and platform for metabolite annotation for imaging mass spectrometry

omnipath-client

Python client for the new OmniPath web APIs

corems

CoreMS is a comprehensive mass spectrometry software framework

mwtab

The mwtab package is a Python library that facilitates reading and writing files in mwTab format used by the Metabolomics Workbench for archival of Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) experimental data.

pygoslin

Python implementation for Goslin

isocor

IsoCor: Isotope Correction for mass spectrometry labeling experiments

ms-mint

Python library for large-scale targeted metabolomics.

pymultiomics

Python toolbox for multi-omics data mapping and analysis

msbuddy

a python package for molecular formula analysis in MS-based small molecule studies

mbpls

(Multiblock) Partial Least Squares Regression for Python

sspa

Single sample pathway analysis tools for omics data

ms-mint-app

Metabolomics Integrator Interactive Web-Application (Mint)

dimepy

Python package for the high-throughput nontargeted metabolite fingerprinting of nominal mass direct injection mass spectrometry directly from mzML files.

dimet

Differential analysis of targeted Isotope-labeled Metabolomics data

npyc

National Phenome Centre toolbox

nplinker

A python framework for microbial natural products data mining by integrating genomics and metabolomics data

find-mfs

A Python package for finding molecular formulae candidates which fit some given mass (+/- an error window). Uses Böcker & Lipták's highly efficient algorithm, as implemented in SIRIUS. This package also implements methods for filtering MF candidates by chemical rules, and simulated isotope envelopes.