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    28 repositories

    • bppg

      Public
      R Package for bipartite peptide-protein graphs
      R
      •
      Other
      •0•3•20•0•Updated Sep 22, 2025Sep 22, 2025

    • McQuaC

      Public
      Transform the Quality Control workflow from Knime into a workflow in Nextflow
      Jupyter Notebook
      •
      Other
      •0•2•35•2•Updated Sep 16, 2025Sep 16, 2025

    • unbeQuant

      Public
      unbeQuant - An unknown (not identified) MS1-Feature Quantification Workflow
      Python
      •0•0•1•0•Updated Sep 3, 2025Sep 3, 2025

    • ProtStatsWF

      Public
      Statistics Workflows for Proteomics Data
      R
      •
      Other
      •0•2•26•0•Updated Aug 22, 2025Aug 22, 2025

    • CalibraCurve

      Public
      CalibraCurve
      calibrationtargeted-proteomicsassaysquantification-limitsdynamic-linear-ranges
      R
      •
      Other
      •2•4•5•0•Updated Jul 30, 2025Jul 30, 2025

    • ProtGraph

      Public
      ProtGraph - A Graph-Generator for Proteins
      pypipython3biocondagraphproteinfastauniprotpeptide
      Python
      •
      Other
      •8•13•9•0•Updated Jul 29, 2025Jul 29, 2025

    • xic-extractor

      Public
      A XIC-Extractor workflow written in Python/nextflow. Simply extract XICs by providing a CSV with an option to plot the XICs in plotly.
      Python
      •
      Other
      •0•0•0•0•Updated Jul 16, 2025Jul 16, 2025

    • CalibraCurve_NF

      Public
      Nextflow workflow for CalibraCurve
      R
      •0•0•0•0•Updated Jun 27, 2025Jun 27, 2025

    • predict_vancomycin

      Public
      0•0•0•0•Updated May 7, 2025May 7, 2025

    • ProGFASTAGen

      Public
      Protein-Graph-FASTA-Generation and Identification
      C++
      •
      Other
      •0•2•0•1•Updated Apr 22, 2025Apr 22, 2025

    • bioinfomatics_for_proteomics_tutorial_data

      Public
      This is just data.
      0•0•0•0•Updated Jan 16, 2025Jan 16, 2025

    • ProtStatsWF_NF

      Public
      Nextflow scripts and workflows related to the ProtStatsWF R package for statistical analysis and visualization of proteomics data
      Jupyter Notebook
      •0•0•3•0•Updated Aug 8, 2024Aug 8, 2024

    • bipartite-peptide-protein-graphs

      Public
      R
      •
      Other
      •0•2•0•0•Updated Jul 9, 2024Jul 9, 2024

    • nf-cloud

      Public archive
      A web interface for Nextflow
      Python
      •10•1•0•0•Updated Jun 27, 2024Jun 27, 2024

    • macpepdb

      Public
      Python
      •2•4•0•0•Updated Feb 29, 2024Feb 29, 2024

    • macpepdb-web

      Public
      Vue
      •0•0•2•0•Updated Oct 18, 2023Oct 18, 2023

    • denbi_summerschool2023_py_exercises

      Public
      Python exercises for the de.NBI Summer School 2023
      Jupyter Notebook
      •0•0•1•0•Updated Oct 13, 2023Oct 13, 2023

    • QC_Quant

      Public
      Quality control for quantitative proteomics data
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 5, 2023Oct 5, 2023

    • pia

      Public
      📚 🔬 PIA - Protein Inference Algorithms
      Java
      •
      Other
      •9•1•0•0•Updated Aug 17, 2023Aug 17, 2023

    • pia-knime-nodes

      Public
      This repository holds the declaration for KNIME nodes to use PIA
      Java
      •5•0•0•0•Updated Jul 11, 2023Jul 11, 2023

    • bacterial-proteogenomic-pipeline

      Public archive
      [DEPRECATED] The Bacterial Proteogenomic Pipeline
      Java
      •
      Other
      •1•0•0•0•Updated Oct 26, 2021Oct 26, 2021

    • ProtGraphREST

      Public
      A REST-API for generated protein graphs
      Python
      •
      Other
      •1•1•0•0•Updated Oct 20, 2021Oct 20, 2021

    • bionda

      Public
      The biomarker database BIONDA performs text mining tasks using a dictioanry approach to identify diseases and poteincial biomarkers (lncRna, proteins, mirna and genes) in Europe PMC abstracts. The RE is sentence-based.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•1•1•1•Updated Oct 1, 2021Oct 1, 2021

    • FiPSPi

      Public
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jun 1, 2021Jun 1, 2021

    • pia-tutorial

      Public
      Tutorial for PIA - Protein Inference Algorithms
      tutorialproteomics
      TeX
      •3•1•0•0•Updated Nov 12, 2020Nov 12, 2020

    • max-decoy

      Public
      Rust
      •0•1•1•0•Updated Apr 3, 2020Apr 3, 2020

    • pia-web-interface

      Public archive
      The web interface source for PIA
      Java
      •
      Other
      •0•0•0•0•Updated Oct 15, 2019Oct 15, 2019

    • PQI

      Public archive
      Java
      •1•0•0•0•Updated Feb 7, 2018Feb 7, 2018