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    28 repositories

    • ProSIMSIt

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

    • 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
      •0•0•1•0•Updated Jul 25, 2025Jul 25, 2025

    • topas-portal

      Public
      Exploratory web-based tool for clinical proteomics TOPAS platform
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 10, 2025Jun 10, 2025

    • enrichment-server

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

    • SIMSI-Transfer

      Public
      Similarity-based Isobaric MS2 Identification Transfer
      Python
      •
      Apache License 2.0
      •3•2•8•0•Updated May 26, 2025May 26, 2025

    • curve_curator

      Public
      Analysis platform for large-scale dose-dependent data
      bioinformaticsstatisticsdashboardanalysisp-valuecurve-fittingproteomicsdose-responseviabilitydecryptm
      Python
      •
      Apache License 2.0
      •4•25•3•0•Updated May 24, 2025May 24, 2025

    • picked_group_fdr

      Public
      Scalable, accurate and sensitive protein group FDRs for large-scale mass spectrometry experiments
      Jupyter Notebook
      •
      Apache License 2.0
      •5•12•6•0•Updated May 23, 2025May 23, 2025

    • 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•2•0•Updated May 21, 2025May 21, 2025

    • biowc-pathwaygraph

      Public
      Interactive Visualization of Signaling Pathways
      TypeScript
      •
      Apache License 2.0
      •0•3•0•0•Updated Feb 19, 2025Feb 19, 2025

    • pathway-importer

      Public
      Download and Convert Pathways from KEGG and WikiPathways
      Python
      •
      Apache License 2.0
      •0•1•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•9•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 cite "Gessulat, Schmidt et al. 2019" DOI 10.1038/s41592-019-0426-7
      Python
      •
      Apache License 2.0
      •46•88•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
      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
      •22•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
      •111•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 of drug action. We extend this paradigm to measuring proteome activity landscapes by acquiring and integrating quantitative data for 10,000 proteins and 55,000 phosphorylation sites (p-s…
      R
      •
      Apache License 2.0
      •2•6•0•0•Updated Apr 21, 2020Apr 21, 2020

    • MasterSpectrum

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

    • cindeR

      Public
      shinycurveclassification
      R
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Jan 23, 2019Jan 23, 2019

    • curveClassification_shiny

      Public
      machine-learningshinycurveclassification
      R
      •
      GNU General Public License v3.0
      •0•1•1•0•Updated Jan 7, 2019Jan 7, 2019