Repositories list

• ms2deepscore

  Public
  Deep learning similarity measure for comparing MS/MS spectra with respect to their chemical similarity

  Jupyter Notebook

  •

  Apache License 2.0

  •30•80•6•2•Updated Mar 26, 2026Mar 26, 2026

• matchms

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

  analysisfuzzy-searchfuzzy-matching+ 4

  analysisfuzzy-searchfuzzy-matchingpython3similarity-measuresmetabolomicsmass-spectrometry

  Python

  •

  Apache License 2.0

  •77•252•21•12•Updated Mar 26, 2026Mar 26, 2026

• graphconstructor

  Public
  Construction of graphs from similarity or distance metrics.

  Python

  •

  MIT License

  •0•1•5•4•Updated Mar 25, 2026Mar 25, 2026

• ms2query_2

  Public
  Library for efficient fast search of unknown MS/MS spectra against a large reference dataset.

  Python

  •

  MIT License

  •0•0•1•3•Updated Mar 24, 2026Mar 24, 2026

• chemap

  Public
  Library for computing molecular fingerprint based similarities as well as dimensionality-reduction-based chemical space visualizations.

  cheminformaticsdata-visualization

  cheminformaticsdata-visualization

  Python

  •

  MIT License

  •1•5•3•0•Updated Mar 9, 2026Mar 9, 2026

• sparsestack

  Public
  Memory efficient stack of multiple 2D sparse arrays.

  Python

  •

  MIT License

  •5•4•6•2•Updated May 26, 2025May 26, 2025

• similarity-graph-generator

  Public
  Generation and processing of a graph from pairwise similarity measures.

  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Feb 11, 2025Feb 11, 2025

• matchms-docs

  Public
  User documentation and tutorial material for matchms

  Jupyter Notebook

  •

  Other

  •0•2•1•0•Updated Jun 13, 2024Jun 13, 2024

• matchmsextras

  Public
  additional network analysis functions for matchms

  Python

  •

  Apache License 2.0

  •2•6•6•2•Updated Aug 22, 2023Aug 22, 2023

• matchms-backup

  Public archive
  Python library for fuzzy comparison of mass spectrum data and other Python objects

  pythonfuzzy-searchfuzzy-matching+ 2

  pythonfuzzy-searchfuzzy-matchingsimilarity-measuresmass-spectrometry

  Python

  •

  Apache License 2.0

  •4•0•0•0•Updated May 20, 2020May 20, 2020

• old-iomega-spec2vec

  Public archive
  unrefactored spec2vec code from iomega org

  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Apr 11, 2020Apr 11, 2020

• notebooks

  Public archive
  Jupyter notebook with matchms tutorial.

  Jupyter Notebook

  •

  Apache License 2.0

  •1•2•0•0•Updated Apr 6, 2020Apr 6, 2020