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    43 repositories

    • mzLib

      Public
      Library for mass spectrometry projects
      chemistrymass-spectrometrychemical-formulas
      chemistrymass-spectrometrychemical-formulasisotopesproteomics-dataspectra-filesproteogenomicsmass-spectrometry-data
      C#
      •
      GNU Lesser General Public License v3.0
      •42•28•73•58•Updated Aug 5, 2026Aug 5, 2026

    • pyMzLib

      Public
      mzLib for Python - mass spectrometry and proteomics from the mzLib C# library, with no .NET to install
      pythonbioinformaticscsharp
      pythonbioinformaticscsharpdotnetproteomicsmass-spectrometrypride-archivemzlib
      C#
      •
      GNU Lesser General Public License v3.0
      •2•0•0•2•Updated Aug 5, 2026Aug 5, 2026

    • mzLibR

      Public
      mzLib for R - mass spectrometry and proteomics, with no .NET to install and no package dependencies
      R
      •
      Other
      •0•0•0•2•Updated Aug 5, 2026Aug 5, 2026

    • mzLibRust

      Public
      mzLib for Rust — mass spectrometry and proteomics, over the same language-neutral bridge as pyMzLib.
      Rust
      •
      GNU Lesser General Public License v3.0
      •0•0•0•2•Updated Aug 5, 2026Aug 5, 2026

    • MetaMorpheus

      Public
      Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
      discoverycalibrationproteome
      discoverycalibrationproteomespectraptmdatabase-searchuniprotmass-matchproteomics-database-search
      C#
      •
      MIT License
      •51•111•209•49•Updated Aug 4, 2026Aug 4, 2026

    • pyMetaMorpheus

      Public
      MetaMorpheus, callable from Python — a dependency-free, faithful projection of the MetaMorpheus CLI.
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 4, 2026Aug 4, 2026

    • ProteaseGuru

      Public
      C#
      •
      GNU General Public License v3.0
      •7•4•8•2•Updated Aug 3, 2026Aug 3, 2026

    • MS_Spectral_Encoding

      Public
      A tutorial on how to encode mass spectra for machine learning
      Jupyter Notebook
      •1•1•0•0•Updated Jun 18, 2026Jun 18, 2026

    • ProteoformExplorer

      Public
      Proteoform Dashboard
      C#
      •
      MIT License
      •4•0•13•0•Updated Apr 13, 2026Apr 13, 2026

    • FlashLFQ

      Public
      Ultra-fast label-free quantification algorithm for mass-spectrometry proteomics
      chemistryproteomicsmass-spectrometry
      chemistryproteomicsmass-spectrometryquantification
      C#
      •
      GNU Lesser General Public License v3.0
      •16•25•38•9•Updated Apr 8, 2026Apr 8, 2026

    • Jenkins-MetaMorpheus

      Public
      Code used for continuous builds of MetaMorpheus
      C#
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated May 16, 2025May 16, 2025

    • mzLib2

      Public
      Library for mass spectrometry projects
      C#
      •
      GNU Lesser General Public License v3.0
      •42•0•0•0•Updated Apr 15, 2025Apr 15, 2025

    • ProteoformSuite

      Public
      Construction, quantification, and visualization of proteoform families
      visualizationcytoscapequantification
      visualizationcytoscapequantificationproteomeptmproteoformproteoform-families
      C#
      •
      GNU General Public License v3.0
      •21•14•23•1•Updated Dec 16, 2024Dec 16, 2024

    • Spritz

      Public
      Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
      bioinformaticsrna-seqsnakemake
      bioinformaticsrna-seqsnakemakeproteomicsproteogenomicssnakemake-pipeline
      C#
      •
      MIT License
      •10•7•26•0•Updated Jun 19, 2024Jun 19, 2024

    • MetaPAL

      Public
      A framework for reading and writing ML-ready proteomics data
      C#
      •
      Apache License 2.0
      •7•0•3•4•Updated Apr 15, 2024Apr 15, 2024

    • MetaNetwork

      Public
      HTML
      •5•12•7•1•Updated Jan 14, 2023Jan 14, 2023

    • SnpEff

      Public
      This is a customized version of SnpEff used in Spritz (https://github.com/smith-chem-wisc/Spritz), which outputs a protein FASTA and XML files that can be used …
      Java
      •85•2•0•0•Updated Jan 12, 2023Jan 12, 2023

    • RawFileReader

      Public
      C#
      •30•0•0•0•Updated Jul 12, 2022Jul 12, 2022

    • mzLib-rest

      Public
      Library for mass spectrometry projects
      C#
      •
      GNU Lesser General Public License v3.0
      •42•0•0•0•Updated Jul 7, 2022Jul 7, 2022

    • AppleTurnover

      Public
      Application for Elucidating Turnover Rates
      C#
      •
      MIT License
      •4•0•1•0•Updated Feb 15, 2022Feb 15, 2022

    • LncRNA-Snakemake

      Public
      The full LncRNA data analysis workflow from sample.fastq to IsoMat.txt
      Python
      •0•0•0•0•Updated Dec 16, 2021Dec 16, 2021

    • ProteoformClassifier

      Public
      Classifies proteoform identifications and validates that input is transparent about ambiguity
      C#
      •
      MIT License
      •1•1•1•0•Updated Aug 10, 2021Aug 10, 2021

    • psi-mod-CV

      Public
      Reactivated PSI-MOD ontology for molecular mass modifications
      19•0•0•0•Updated Dec 8, 2020Dec 8, 2020

    • MetaDrive

      Public
      C#
      •3•0•0•0•Updated Sep 9, 2020Sep 9, 2020

    • Learning-CSharp

      Public
      A Course for Learning the C# Programming Language
      MIT License
      •0•0•0•0•Updated May 11, 2020May 11, 2020

    • HackyButFunctionalCodeToMakeLifeEasier

      Public
      The name says it all. Made public by Lei's request. Use at your own risk.
      C#
      •0•0•0•0•Updated Aug 29, 2019Aug 29, 2019

    • ProteoformSuiteVignettes

      Public
      Vignettes for Proteoform Suite
      2•0•0•0•Updated May 16, 2019May 16, 2019

    • Proteogenomics

      Public
      C# implementation of classes and functions for proteogenomics
      C#
      •2•1•2•0•Updated Mar 30, 2019Mar 30, 2019

    • ThermoRawFileParser

      Public
      Thermo RAW file parser that runs on Linux with mono
      C#
      •
      Other
      •60•0•0•0•Updated Oct 22, 2018Oct 22, 2018

    • MetaMorpheus-Peptide-Database-Generator

      Public
      Creates a .fasta database from MetaMorpheus PSM results
      MIT License
      •0•0•0•0•Updated Oct 12, 2018Oct 12, 2018
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