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    32 repositories

    • topas-pipeline

      Public
      Automated (phospho)proteomics processing pipeline for large patient cohorts providing cohort as well as patient-specific insights.
      Python
      •
      Apache License 2.0
      •1•1•3•0•Updated Sep 4, 2026Sep 4, 2026

    • picked_group_fdr

      Public
      Scalable, accurate and sensitive protein group FDRs for large-scale mass spectrometry experiments
      Jupyter Notebook
      •
      Apache License 2.0
      •5•14•4•0•Updated Aug 20, 2026Aug 20, 2026

    • SIMSI-Transfer

      Public
      Similarity-based Isobaric MS2 Identification Transfer
      Python
      •
      Apache License 2.0
      •4•3•9•0•Updated Jul 24, 2026Jul 24, 2026

    • topas-portal

      Public
      Exploratory web-based tool for clinical proteomics TOPAS platform
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jul 20, 2026Jul 20, 2026

    • topas-manuscript-figures

      Public
      Data analysis and plotting scripts for the TOPAS manuscripts.
      Jupyter Notebook
      •0•0•0•0•Updated Jul 14, 2026Jul 14, 2026

    • psite_annotation

      Public
      Python module for annotating a pandas dataframe with phosphosites, e.g. PhosphoSitePlus annotations, kinase-substrate relations, domain information, etc.
      Python
      •
      Apache License 2.0
      •0•4•3•0•Updated Jul 2, 2026Jul 2, 2026

    • astral_mcp

      Public
      Python
      •0•0•0•0•Updated May 26, 2026May 26, 2026

    • icorr

      Public
      Identity correlation coefficient
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 7, 2026Apr 7, 2026

    • biowc-pathwaygraph

      Public
      Interactive Visualization of Signaling Pathways
      TypeScript
      •
      Apache License 2.0
      •0•3•0•1•Updated Mar 16, 2026Mar 16, 2026

    • ptmnavigator

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •0•1•0•0•Updated Feb 2, 2026Feb 2, 2026

    • curve_curator

      Public
      Analysis platform for large-scale dose-dependent data
      bioinformaticsstatisticsdashboard
      bioinformaticsstatisticsdashboardanalysisp-valuecurve-fittingproteomicsdose-responseviabilitydecryptm
      Python
      •
      Apache License 2.0
      •8•31•6•0•Updated Nov 25, 2025Nov 25, 2025

    • ProSIMSIt

      Public
      Python
      •
      Apache License 2.0
      •0•3•0•0•Updated Jul 31, 2025Jul 31, 2025

    • enrichment-server

      Public
      HTML
      •
      Apache License 2.0
      •0•1•0•0•Updated Jun 3, 2025Jun 3, 2025

    • pathway-importer

      Public
      Download and Convert Pathways from KEGG and WikiPathways
      Python
      •
      Apache License 2.0
      •0•2•0•0•Updated Nov 27, 2024Nov 27, 2024

    • Gem_synergy

      Public
      Code to analyze and plot data from S. Hoefer et al. 2024.
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Sep 18, 2024Sep 18, 2024

    • TIC_Normalization

      Public
      R script and exemplary input and output files for the TIC normalization approach.
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Aug 22, 2024Aug 22, 2024

    • use_embedded

      Public
      Go
      •1•0•0•0•Updated Jul 10, 2024Jul 10, 2024

    • decryptM

      Public
      Python
      •
      MIT License
      •1•8•0•0•Updated Sep 7, 2023Sep 7, 2023

    • prosit

      Public archive
      Prosit offers high quality MS2 predicted spectra for any organism and protease as well as iRT prediction. When using Prosit is helpful for your research, please…
      Python
      •
      Apache License 2.0
      •45•92•23•1•Updated Aug 17, 2023Aug 17, 2023

    • IPSA_helper

      Public
      JavaScript
      •0•2•3•4•Updated Mar 3, 2023Mar 3, 2023

    • curveClassification_package

      Public
      curveclassification
      curveclassification
      R
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated May 9, 2022May 9, 2022

    • proteomicsdb-vue-workshop

      Public
      Vue
      •
      Apache License 2.0
      •0•1•0•0•Updated Mar 22, 2022Mar 22, 2022

    • universal_spectrum_explorer

      Public
      JavaScript
      •
      MIT License
      •6•15•1•0•Updated Jan 27, 2022Jan 27, 2022

    • iapi

      Public
      Instrument Application Programming Interface
      MIT License
      •25•1•0•0•Updated Jan 25, 2022Jan 25, 2022

    • proteomicsJS

      Public
      JavaScript
      •
      MIT License
      •0•1•1•0•Updated Apr 27, 2021Apr 27, 2021

    • IPSA

      Public
      The Interactive Peptide Spectral Annotator
      JavaScript
      •
      MIT License
      •9•0•0•0•Updated Oct 20, 2020Oct 20, 2020

    • pxdUSIbrowser

      Public
      MIT License
      •0•0•0•0•Updated Oct 20, 2020Oct 20, 2020

    • proteomics-metadata-standard

      Public
      The Proteomics Experimental Design file format: Standard for experimental design annotation
      Shell
      •115•1•0•0•Updated Jun 4, 2020Jun 4, 2020

    • ATLANTiC

      Public
      Integrated analysis of genomes, transcriptomes, proteomes and drug responses of cancer cell lines (CCLs) is an emerging approach to uncover molecular mechanisms…
      R
      •
      Apache License 2.0
      •2•6•0•0•Updated Apr 21, 2020Apr 21, 2020

    • MasterSpectrum

      Public
      pythonproteomicsmgf
      pythonproteomicsmgf
      Python
      •
      MIT License
      •0•3•0•0•Updated Mar 11, 2020Mar 11, 2020
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