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    60 repositories

    • quantmsdiann

      Public
      quantms workflow for DIANN tool including DIA and DDA analysis
      Nextflow
      •
      MIT License
      •6•7•3•1•Updated Apr 21, 2026Apr 21, 2026

    • msgfplus

      Public
      MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
      search-engineproteomicsmass-spectrometry
      search-engineproteomicsmass-spectrometrysequential-algorithm
      Java
      •
      Other
      •37•1•0•1•Updated Apr 21, 2026Apr 21, 2026

    • quantms

      Public
      Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quant…
      proteomicsmass-spectrometryproteogenomics
      proteomicsmass-spectrometryproteogenomicstmtlfq
      Nextflow
      •
      MIT License
      •54•71•53•1•Updated Apr 21, 2026Apr 21, 2026

    • sdrf-annotated-datasets

      Public
      A repository of datasets in ProteomeXchange annotated in SDRF, previously part of the specification
      Python
      •
      Apache License 2.0
      •0•2•0•0•Updated Apr 20, 2026Apr 20, 2026

    • sdrf-templates

      Public
      SDRF templates and validation yaml files from specification proteomics-sample-metadata
      Python
      •
      Apache License 2.0
      •8•1•1•4•Updated Apr 20, 2026Apr 20, 2026

    • qpx

      Public
      qpx (Quantitative Proteomics eXchange) format (aka quantms.io) a format to capture a full proteomics experiment
      Python
      •
      Apache License 2.0
      •6•18•25•0•Updated Apr 20, 2026Apr 20, 2026

    • proteomics-sample-metadata

      Public
      The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets
      metadataproteomicsproteomics-datasets
      metadataproteomicsproteomics-datasetsmultiomicsproteomexchangesdrfpride-metadatamsrun-metadatasdrf-proteomicsproteomics-community
      HTML
      •
      GNU General Public License v2.0
      •115•102•43•1•Updated Apr 19, 2026Apr 19, 2026

    • sdrf-skills

      Public
      SDRF skills that enables to perform multiple tasks on SDRF annotations - validations using Claude
      Shell
      •
      MIT License
      •3•2•0•3•Updated Apr 19, 2026Apr 19, 2026

    • sdrfedit

      Public
      lightweight, self hosted javascript editor for sdrf.
      TypeScript
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 19, 2026Apr 19, 2026

    • mokume

      Public
      Integrated library to perform feature normalization and multiple abundance computing based on qpx
      Python
      •
      MIT License
      •2•1•1•0•Updated Apr 18, 2026Apr 18, 2026

    • hvantk

      Public
      Hail variant annotation toolkit
      big-datagenomicshail
      big-datagenomicshailvariant-analysis
      Python
      •
      MIT License
      •0•0•8•1•Updated Apr 18, 2026Apr 18, 2026

    • spectrafuse

      Public
      Incremental clustesting pipeline from quantms data.
      Nextflow
      •
      MIT License
      •0•1•2•0•Updated Apr 18, 2026Apr 18, 2026

    • pyspectrafuse

      Public
      Python library with utility scripts for spectrafuse pipeline
      Python
      •
      Apache License 2.0
      •1•0•0•0•Updated Apr 18, 2026Apr 18, 2026

    • pIR

      Public
      Estimation of isoelectric point of peptides and proteins using support vector machines (SVM).
      machine-learningproteinspeptides
      machine-learningproteinspeptidesisoelectric-point
      R
      •6•10•0•0•Updated Apr 15, 2026Apr 15, 2026

    • quantms-containers

      Public
      DIANN docker container and OpenMS release for quantms
      Dockerfile
      •
      Apache License 2.0
      •5•2•1•1•Updated Apr 15, 2026Apr 15, 2026

    • pmultiqc

      Public
      A library for QC report based on MultiQC framework
      proteomicsmass-spectrometryproteomics-data
      proteomicsmass-spectrometryproteomics-dataqcqc-proteomics
      Python
      •
      MIT License
      •22•30•6•1•Updated Apr 14, 2026Apr 14, 2026

    • sdrf-pipelines

      Public
      `sdrf-pipelines` is the official SDRF file validator and converts SDRF to pipeline configuration files
      proteomicsmass-spectrometryopenms
      proteomicsmass-spectrometryopenmsmaxquantmsstatsmultiomicssdrfproteomics-data-analysis
      Python
      •
      Apache License 2.0
      •29•31•38•1•Updated Apr 14, 2026Apr 14, 2026

    • quantms-rescoring

      Public
      quantms and ms2rescore helper functions and scripts
      Python
      •
      Apache License 2.0
      •1•1•0•0•Updated Apr 13, 2026Apr 13, 2026

    • quantms-utils

      Public
      A python library with scripts and helpers classes for quantms workflow
      cloudnextflowbigdata
      cloudnextflowbigdataproteomicsmass-spectrometryproteogenomics
      Python
      •
      MIT License
      •5•6•0•1•Updated Apr 13, 2026Apr 13, 2026

    • quantms-portal

      Public
      Tooling and frontend for portal.quantms.org — AI-first proteomics data portal
      Vue
      •0•0•0•0•Updated Apr 13, 2026Apr 13, 2026

    • quantms.org

      Public
      Web page storing all the datasets renalyzed with quantms
      HTML
      •
      MIT License
      •4•0•0•0•Updated Apr 13, 2026Apr 13, 2026

    • fslite

      Public
      Lightweight Feature selection Python library
      scikit-learnfeature-selectionmultiomics
      scikit-learnfeature-selectionmultiomics
      Python
      •
      Apache License 2.0
      •1•1•4•0•Updated Apr 8, 2026Apr 8, 2026

    • quantms-test-datasets

      Public
      Python
      •
      MIT License
      •2•2•0•0•Updated Apr 7, 2026Apr 7, 2026

    • relink

      Public
      A nextflow workflow for the analysis of large-scale crosslinking experiments
      Nextflow
      •
      MIT License
      •1•0•6•1•Updated Apr 7, 2026Apr 7, 2026

    • crosslinking-datasets

      Public
      Crosslinking datasets to be annotated
      Python
      •0•0•0•1•Updated Mar 30, 2026Mar 30, 2026

    • nf-modules

      Public
      quantms and other bigbio workflows modules in nf-core, nextflow standards
      Nextflow
      •
      MIT License
      •3•0•0•0•Updated Mar 23, 2026Mar 23, 2026

    • techsdrf

      Public
      techSDRF
      Python
      •
      Apache License 2.0
      •1•0•0•0•Updated Mar 18, 2026Mar 18, 2026

    • pgatk

      Public
      Python tools for proteogenomics analysis toolkit
      pythonvcfensembl
      pythonvcfensemblproteomicsmass-spectrometryproteogenomicsproteogenomics-analysis-toolkit
      Python
      •
      Apache License 2.0
      •13•15•2•0•Updated Mar 4, 2026Mar 4, 2026

    • quantms-readthedocs

      Public
      This repository contains the documentation of quantms workflow
      Batchfile
      •
      MIT License
      •3•0•0•1•Updated Feb 21, 2026Feb 21, 2026

    • Kaggle-Harmonizing-the-data-of-your-data

      Public
      Repository for the NCEMS sponsored Kaggle competition.
      Python
      •
      GNU General Public License v3.0
      •22•0•0•0•Updated Jan 31, 2026Jan 31, 2026
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