Repositories list

• sdrf-skills

  Public

  bigbio/sdrf-skills’s past year of commit activity
  SDRF skills that enables to perform multiple tasks on SDRF annotations - validations using Claude

  MIT License

  •0•0•0•0•Updated Mar 18, 2026Mar 18, 2026

• techsdrf

  Public
  techSDRF

  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Mar 18, 2026Mar 18, 2026

• quantmsdiann

  Public
  quantms workflow for DIANN tool including DIA and DDA analysis

  MIT License

  •3•0•11•0•Updated Mar 18, 2026Mar 18, 2026

• sdrfedit

  Public
  lightweight, self hosted javascript editor for sdrf.

  TypeScript

  •

  Apache License 2.0

  •0•0•1•1•Updated Mar 18, 2026Mar 18, 2026

• pmultiqc

  Public
  A library for QC report based on MultiQC framework

  proteomicsmass-spectrometryproteomics-data+ 2

  proteomicsmass-spectrometryproteomics-dataqcqc-proteomics

  Python

  •

  MIT License

  •21•29•5•1•Updated Mar 18, 2026Mar 18, 2026

• proteomics-sample-metadata

  Public
  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

  •116•100•50•1•Updated Mar 18, 2026Mar 18, 2026

• quantms-containers

  Public
  DIANN docker container and OpenMS release for quantms

  Dockerfile

  •

  Apache License 2.0

  •4•2•0•0•Updated Mar 18, 2026Mar 18, 2026

• mokume

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

  Python

  •

  MIT License

  •2•1•1•1•Updated Mar 17, 2026Mar 17, 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

  •54•68•64•2•Updated Mar 17, 2026Mar 17, 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•16•22•0•Updated Mar 16, 2026Mar 16, 2026

• hvantk

  Public
  Hail variant annotation toolkit

  big-datagenomicshail+ 1

  big-datagenomicshailvariant-analysis

  Python

  •

  MIT License

  •0•0•11•0•Updated Mar 16, 2026Mar 16, 2026

• nf-modules

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

  Nextflow

  •

  MIT License

  •3•0•2•1•Updated Mar 14, 2026Mar 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

  •29•29•37•0•Updated Mar 13, 2026Mar 13, 2026

• sdrf-templates

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

  Python

  •

  Apache License 2.0

  •5•1•1•1•Updated Mar 13, 2026Mar 13, 2026

• crosslinking-datasets

  Public
  Crosslinking datasets to be annotated

  Python

  •0•0•0•0•Updated Mar 11, 2026Mar 11, 2026

• quantms.org

  Public
  Web page storing all the datasets renalyzed with quantms

  Vue

  •

  MIT License

  •4•0•0•0•Updated Mar 11, 2026Mar 11, 2026

• pgatk

  Public
  Python tools for proteogenomics analysis toolkit

  pythonvcfensembl+ 4

  pythonvcfensemblproteomicsmass-spectrometryproteogenomicsproteogenomics-analysis-toolkit

  Python

  •

  Apache License 2.0

  •13•15•2•0•Updated Mar 4, 2026Mar 4, 2026

• quantms-rescoring

  Public
  quantms and ms2rescore helper functions and scripts

  Python

  •

  Apache License 2.0

  •1•1•0•0•Updated Mar 2, 2026Mar 2, 2026

• quantms-test-datasets

  Public
  Python

  •

  MIT License

  •2•2•0•0•Updated Feb 28, 2026Feb 28, 2026

• relink

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

  Nextflow

  •

  MIT License

  •1•0•0•0•Updated Feb 26, 2026Feb 26, 2026

• quantms-utils

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

  cloudnextflowbigdata+ 3

  cloudnextflowbigdataproteomicsmass-spectrometryproteogenomics

  Python

  •

  MIT License

  •4•6•0•0•Updated Feb 26, 2026Feb 26, 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

  •9•0•0•0•Updated Jan 31, 2026Jan 31, 2026

• onsite

  Public
  onsite: posttranslation modification site localization

  Python

  •

  MIT License

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

  proteomicsmass-spectrometryproteomics-data-analysismissing-value-imputation

  Jupyter Notebook

  •

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

  •1•0•0•0•Updated Jan 5, 2026Jan 5, 2026

• 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

• 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