Repositories list

• 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+ 1

  search-engineproteomicsmass-spectrometrysequential-algorithm

  Java

  •

  Other

  •3737 forks•11 star•00 issues•22 pull requests•Updated Apr 26, 2026Apr 26, 2026

• quantms-containers

  Public

  bigbio/quantms-containers’s past year of commit activity
  DIANN docker container and OpenMS release for quantms

  Dockerfile

  •

  Apache License 2.0

  •55 forks•33 stars•22 issues•11 pull request•Updated Apr 26, 2026Apr 26, 2026

• quantmsdiann

  Public

  bigbio/quantmsdiann’s past year of commit activity
  quantms workflow for DIANN tool including DIA and DDA analysis

  Nextflow

  •

  MIT License

  •66 forks•88 stars•55 issues•22 pull requests•Updated Apr 24, 2026Apr 24, 2026

• proteomics-sample-metadata

  Public

  bigbio/proteomics-sample-metadata’s past year of commit activity
  SDRF: The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets

  metadataproteomicsproteomics-datasets+ 9

  metadataproteomicsproteomics-datasetsmultiomicsproteomexchangesdrfpride-metadatamsrun-metadatasdrf-proteomicsproteomics-community+ 2

  HTML

  •

  GNU General Public License v2.0

  •115115 forks•102102 stars•4343 issues•11 pull request•Updated Apr 24, 2026Apr 24, 2026

• hvantk

  Public

  bigbio/hvantk’s past year of commit activity
  Hail variant annotation toolkit

  big-datagenomicshail+ 1

  big-datagenomicshailvariant-analysis

  Python

  •

  MIT License

  •00 forks•00 stars•77 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• relink

  Public

  bigbio/relink’s past year of commit activity
  A nextflow workflow for the analysis of large-scale crosslinking experiments

  Nextflow

  •

  MIT License

  •11 fork•00 stars•66 issues•11 pull request•Updated Apr 23, 2026Apr 23, 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+ 2

  proteomicsmass-spectrometryproteogenomicstmtlfq

  Nextflow

  •

  MIT License

  •5656 forks•7272 stars•5353 issues•11 pull request•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

  •00 forks•22 stars•00 issues•00 pull requests•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

  •88 forks•11 star•11 issue•44 pull requests•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

  •66 forks•1818 stars•2626 issues•11 pull request•Updated Apr 20, 2026Apr 20, 2026

• sdrf-skills

  Public
  SDRF skills that enables to perform multiple tasks on SDRF annotations - validations using Claude

  Shell

  •

  MIT License

  •33 forks•33 stars•00 issues•33 pull requests•Updated Apr 19, 2026Apr 19, 2026

• sdrfedit

  Public
  lightweight, self hosted javascript editor for sdrf.

  TypeScript

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 19, 2026Apr 19, 2026

• mokume

  Public
  Integrated library to perform feature normalization and multiple abundance computing based on qpx

  Python

  •

  MIT License

  •22 forks•11 star•11 issue•00 pull requests•Updated Apr 18, 2026Apr 18, 2026

• spectrafuse

  Public
  Incremental clustesting pipeline from quantms data.

  Nextflow

  •

  MIT License

  •00 forks•11 star•22 issues•00 pull requests•Updated Apr 18, 2026Apr 18, 2026

• pyspectrafuse

  Public
  Python library with utility scripts for spectrafuse pipeline

  Python

  •

  Apache License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 18, 2026Apr 18, 2026

• pIR

  Public
  Estimation of isoelectric point of peptides and proteins using support vector machines (SVM).

  machine-learningproteinspeptides+ 1

  machine-learningproteinspeptidesisoelectric-point

  R

  •66 forks•1010 stars•00 issues•00 pull requests•Updated Apr 15, 2026Apr 15, 2026

• pmultiqc

  Public
  A library for QC report based on MultiQC framework

  proteomicsmass-spectrometryproteomics-data+ 2

  proteomicsmass-spectrometryproteomics-dataqcqc-proteomics

  Python

  •

  MIT License

  •2323 forks•3030 stars•77 issues•22 pull requests•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+ 5

  proteomicsmass-spectrometryopenmsmaxquantmsstatsmultiomicssdrfproteomics-data-analysis

  Python

  •

  Apache License 2.0

  •2929 forks•3131 stars•3838 issues•11 pull request•Updated Apr 14, 2026Apr 14, 2026

• quantms-rescoring

  Public
  quantms and ms2rescore helper functions and scripts

  Python

  •

  Apache License 2.0

  •11 fork•11 star•00 issues•00 pull requests•Updated Apr 13, 2026Apr 13, 2026

• quantms-utils

  Public
  A python library with scripts and helpers classes for quantms workflow

  cloudnextflowbigdata+ 3

  cloudnextflowbigdataproteomicsmass-spectrometryproteogenomics

  Python

  •

  MIT License

  •55 forks•66 stars•00 issues•11 pull request•Updated Apr 13, 2026Apr 13, 2026

• quantms-portal

  Public
  Tooling and frontend for portal.quantms.org — AI-first proteomics data portal

  Vue

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 13, 2026Apr 13, 2026

• quantms.org

  Public
  Web page storing all the datasets renalyzed with quantms

  HTML

  •

  MIT License

  •44 forks•00 stars•00 issues•00 pull requests•Updated Apr 13, 2026Apr 13, 2026

• fslite

  Public
  Lightweight Feature selection Python library

  scikit-learnfeature-selectionmultiomics

  scikit-learnfeature-selectionmultiomics

  Python

  •

  Apache License 2.0

  •11 fork•11 star•44 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• quantms-test-datasets

  Public
  Python

  •

  MIT License

  •22 forks•22 stars•00 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• crosslinking-datasets

  Public
  Crosslinking datasets to be annotated

  Python

  •00 forks•00 stars•00 issues•11 pull request•Updated Mar 30, 2026Mar 30, 2026

• nf-modules

  Public
  quantms and other bigbio workflows modules in nf-core, nextflow standards

  Nextflow

  •

  MIT License

  •33 forks•00 stars•00 issues•00 pull requests•Updated Mar 23, 2026Mar 23, 2026

• techsdrf

  Public
  techSDRF

  Python

  •

  Apache License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Mar 18, 2026Mar 18, 2026

• pgatk

  Public
  Python tools for proteogenomics analysis toolkit

  pythonvcfensembl+ 4

  pythonvcfensemblproteomicsmass-spectrometryproteogenomicsproteogenomics-analysis-toolkit

  Python

  •

  Apache License 2.0

  •1313 forks•1515 stars•22 issues•00 pull requests•Updated Mar 4, 2026Mar 4, 2026

• quantms-readthedocs

  Public
  This repository contains the documentation of quantms workflow

  Batchfile

  •

  MIT License

  •33 forks•00 stars•00 issues•11 pull request•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

  •2222 forks•00 stars•00 issues•00 pull requests•Updated Jan 31, 2026Jan 31, 2026