Repositories list

• CoreMS

  Public
  CoreMS is a comprehensive mass spectrometry software framework

  data-analysismetabolomicsmass-spectrometry+ 8

  data-analysismetabolomicsmass-spectrometrydissolved-organic-mattermetabolomics-pipelinemolecular-searchmolecular-formulae-assignmentmolecular-databasecomplex-mixturenatural-organic-matter+ 1

  Python

  •

  BSD 2-Clause "Simplified" License

  •3939 forks•6565 stars•00 issues•88 pull requests•Updated Apr 21, 2026Apr 21, 2026

• Pore2Chip

  Public
  A python package that takes XCT images of porous materials and generates representative digital twin micromodels

  pythonflowmachine-learning+ 17

  pythonflowmachine-learninglabdata-visualizationscientific-visualizationneural-networksdata-analysissoilporous-media+ 10

  Python

  •

  MIT License

  •55 forks•1313 stars•11 issue•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

• AI4Minerals

  Public
  A python package on AI framework and methods for critical minerals and materials applications

  00 forks•00 stars•00 issues•00 pull requests•Updated Mar 2, 2026Mar 2, 2026

• PSpecteR

  Public
  The PSpecteR users manual can be accessed via the weblink below

  HTML

  •11 fork•33 stars•00 issues•11 pull request•Updated Feb 20, 2026Feb 20, 2026

• pspecterlib

  Public
  Proteomics R package for matching peptide fragments for both digested and intact proteomics

  R

  •

  BSD 2-Clause "Simplified" License

  •11 fork•88 stars•11 issue•00 pull requests•Updated Feb 12, 2026Feb 12, 2026

• isoforma-lib

  Public
  R package for the relative quantitation of proteoforms with MS2 fragmentation patterns

  R

  •

  BSD 2-Clause "Simplified" License

  •00 forks•33 stars•11 issue•00 pull requests•Updated Feb 12, 2026Feb 12, 2026

• EnviroMS

  Public
  EnviroMS is a software for natural organic matter data processing and annotation

  Python

  •

  BSD 2-Clause "Simplified" License

  •33 forks•44 stars•00 issues•00 pull requests•Updated Feb 4, 2026Feb 4, 2026

• grip-tomo

  Public
  GRaph Identification of Proteins in TOMOgrams (GRIP-TOMO)

  python

  python

  Python

  •

  BSD 2-Clause "Simplified" License

  •33 forks•44 stars•00 issues•00 pull requests•Updated Nov 19, 2025Nov 19, 2025

• linkml

  Public
  Linked Open Data Modeling Language

  Python

  •

  Other

  •165165 forks•00 stars•00 issues•00 pull requests•Updated Nov 12, 2025Nov 12, 2025

• MetaMS

  Public
  Python

  •

  BSD 2-Clause "Simplified" License

  •11 fork•44 stars•00 issues•00 pull requests•Updated Oct 23, 2025Oct 23, 2025

• ftmsRanalysis

  Public
  R

  •

  Other

  •1111 forks•3333 stars•33 issues•22 pull requests•Updated Jun 10, 2025Jun 10, 2025

• FREDA

  Public
  HTML

  •11 fork•33 stars•33 issues•22 pull requests•Updated Jun 10, 2025Jun 10, 2025

• PIML4PDE

  Public
  A python package for physics-informed machine learning for solving partial differential equations

  pythonmachine-learningneural-networks+ 6

  pythonmachine-learningneural-networksdata-analysiswave-equationmulti-physicsdiffusion-equationporous-mediadarcy-flow

  Other

  •44 forks•1313 stars•00 issues•00 pull requests•Updated Feb 12, 2025Feb 12, 2025

• mapDataAccess-lib

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 6, 2024Aug 6, 2024

• CCSz-demo

  Public
  Python and R scripts with examples demonstrating the conversion of IM-MS raw data to CCS/z space.

  mass-spectrometryccsion-mobility-spectrometry+ 2

  mass-spectrometryccsion-mobility-spectrometrymzapnnl-preprocessor

  Python

  •

  BSD 2-Clause "Simplified" License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Mar 27, 2024Mar 27, 2024

• nmRanalysis

  Public
  R

  •

  Other

  •22 forks•55 stars•00 issues•11 pull request•Updated Jan 24, 2024Jan 24, 2024

• IsoForma-paper

  Public
  HTML

  •00 forks•00 stars•11 issue•00 pull requests•Updated Oct 19, 2023Oct 19, 2023

• CoreMS-AutoUpload

  Public
  Instrument deployed Auto Uploader integrated with CoreMS-Portal.

  Python

  •

  BSD 2-Clause "Simplified" License

  •00 forks•11 star•00 issues•00 pull requests•Updated May 1, 2023May 1, 2023

• PeakDecoder

  Public
  A workflow for metabolite identification and accurate profiling in multidimensional LC-IM-MS-DIA measurements. DOI: 10.5281/zenodo.

  machine-learningmetabolomicsmass-spectrometry+ 3

  machine-learningmetabolomicsmass-spectrometryfalse-discovery-rateion-mobility-spectrometrydata-independent-acquisition

  R

  •

  BSD 2-Clause "Simplified" License

  •44 forks•1616 stars•00 issues•00 pull requests•Updated Apr 25, 2023Apr 25, 2023

• Day3-EMSL-SummerSchool-2022

  Public
  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •11 fork•44 stars•00 issues•00 pull requests•Updated Jul 18, 2022Jul 18, 2022

• CoreMS-Portal

  Public
  JavaScript

  •

  BSD 2-Clause "Simplified" License

  •00 forks•77 stars•00 issues•00 pull requests•Updated Jul 13, 2022Jul 13, 2022

• RBD-intact-peak-analysis

  Public
  R

  •

  BSD 2-Clause "Simplified" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 1, 2022Jul 1, 2022

• MetaCycData

  Public
  R

  •11 fork•22 stars•11 issue•00 pull requests•Updated Oct 11, 2021Oct 11, 2021

• dimpl

  Public
  R

  •

  Other

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 13, 2020Jul 13, 2020