Repositories list

• sdrf-templates

  Public
  SDRF templates and validation yaml files from specification proteomics-sample-metadata

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 29, 2026Jan 29, 2026

• hvantk

  Public
  Hail variant annotation toolkit

  big-datagenomicsbigdata+ 2hailvariant-analysis

  Python

  •

  MIT License

  •0•0•7•1•Updated Jan 29, 2026Jan 29, 2026

• mokume

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

  Python

  •

  MIT License

  •2•1•2•0•Updated Jan 28, 2026Jan 28, 2026

• proteomics-sample-metadata

  Public

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

  metadataproteomicsproteomics-datasets+ 9multiomicsproteomexchangesdrfpride-metadatamsrun-metadatasdrf-proteomicsproteomics-community+ 2

  GNU General Public License v2.0

  •113•101•87•2•Updated Jan 28, 2026Jan 28, 2026

• sdrf-pipelines

  Public

  bigbio/sdrf-pipelines’s past year of commit activity
  `sdrf-pipelines` is the official SDRF file validator and converts SDRF to pipeline configuration files

  proteomicsmass-spectrometryopenms+ 5maxquantmsstatsmultiomicssdrfproteomics-data-analysis

  Python

  •

  Apache License 2.0

  •27•29•39•1•Updated Jan 26, 2026Jan 26, 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•14•20•0•Updated Jan 25, 2026Jan 25, 2026

• pmultiqc

  Public

  bigbio/pmultiqc’s past year of commit activity
  A library for QC report based on MultiQC framework

  proteomicsmass-spectrometryproteomics-data+ 2qcqc-proteomics

  Python

  •

  MIT License

  •19•26•9•0•Updated Jan 23, 2026Jan 23, 2026

• onsite

  Public
  onsite: posttranslation modification site localization

  Python

  •

  MIT License

  •1•2•1•1•Updated Jan 22, 2026Jan 22, 2026

• quantms

  Public

  bigbio/quantms’s past year of commit activity
  Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

  proteomicsmass-spectrometryproteogenomics+ 2tmtlfq

  Nextflow

  •

  MIT License

  •52•65•65•1•Updated Jan 21, 2026Jan 21, 2026

• quantms-test-datasets

  Public
  Python

  •

  MIT License

  •1•0•0•0•Updated Jan 20, 2026Jan 20, 2026

• quantms-readthedocs

  Public
  This repository contains the documentation of quantms workflow

  Batchfile

  •

  MIT License

  •2•0•0•0•Updated Jan 17, 2026Jan 17, 2026

• quantms-containers

  Public
  DIANN docker container and OpenMS release for quantms

  Dockerfile

  •

  Apache License 2.0

  •3•2•0•1•Updated Jan 9, 2026Jan 9, 2026

• spectrafuse

  Public
  Incremental clustesting pipeline from quantms data.

  Nextflow

  •

  MIT License

  •0•1•2•0•Updated Jan 8, 2026Jan 8, 2026

• pyspectrafuse

  Public
  Python library with utility scripts for spectrafuse pipeline

  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Jan 7, 2026Jan 7, 2026

• GainPro

  Public
  GainPro is a PyTorch implementation of Generative Adversarial Imputation Networks (GAIN) for imputing missing iBAQ values in proteomics datasets.

  proteomicsmass-spectrometryproteomics-data-analysis+ 1missing-value-imputation

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •2•0•0•0•Updated Jan 5, 2026Jan 5, 2026

• nf-modules

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

  Nextflow

  •

  MIT License

  •2•0•2•0•Updated Jan 5, 2026Jan 5, 2026

• quantms-rescoring

  Public
  quantms and ms2rescore helper functions and scripts

  Python

  •

  Apache License 2.0

  •1•1•0•0•Updated Jan 4, 2026Jan 4, 2026

• py-pgatk

  Public
  Python tools for proteogenomics analysis toolkit

  pythonvcfensembl+ 4proteomicsmass-spectrometryproteogenomicsproteogenomics-analysis-toolkit

  Python

  •

  Apache License 2.0

  •13•13•9•0•Updated Jan 3, 2026Jan 3, 2026

• relink

  Public
  A nextflow workflow for the analysis of large-scale crosslinking experiments

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Jan 2, 2026Jan 2, 2026

• crosslinking-datasets

  Public
  Crosslinking datasets to be annotated

  Python

  •0•0•0•0•Updated Dec 14, 2025Dec 14, 2025

• pycross

  Public
  Crosslinking workflow

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 10, 2025Dec 10, 2025

• .github

  Public
  MIT License

  •0•0•0•0•Updated Dec 5, 2025Dec 5, 2025

• quantms-utils

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

  cloudnextflowbigdata+ 3proteomicsmass-spectrometryproteogenomics

  Python

  •

  MIT License

  •4•5•0•0•Updated Nov 27, 2025Nov 27, 2025

• scalefreeqc

  Public
  This library enables to compute idfree QC metrics for mzML files using pyopenms

  Jupyter Notebook

  •

  MIT License

  •1•1•0•0•Updated Nov 19, 2025Nov 19, 2025

• quantms-rescoring-paper

  Public
  TeX

  •

  Creative Commons Zero v1.0 Universal

  •6•1•0•0•Updated Oct 11, 2025Oct 11, 2025

• ibaqpy

  Public
  Absolute quantification package based on quantms.io

  proteomicsmass-spectrometryquantification+ 2absolute-quantificationibaq

  HTML

  •

  MIT License

  •13•16•4•0•Updated Sep 25, 2025Sep 25, 2025

• SDRFscribe

  Public
  AI assistant of SDRF annotations.

  Apache License 2.0

  •1•0•0•1•Updated Jul 11, 2025Jul 11, 2025

• DLEAMSE

  Public
  A Deep LEArning-based Mass Spectra Embedder for spectral similarity scoring

  Python

  •

  Apache License 2.0

  •4•11•3•1•Updated Jun 18, 2025Jun 18, 2025

• quantms.org

  Public
  Web page storing all the datasets renalyzed with quantms

  Vue

  •

  MIT License

  •4•0•0•0•Updated Jun 2, 2025Jun 2, 2025

• sdrf-cellline-metadata-db

  Public
  SDRF Cell Line Metadata Database

  metadataannotationsproteomics+ 5mass-spectrometryhupo-psisdrfsdrf-proteomicscelllines

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 20, 2025Jan 20, 2025