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    41 repositories

    • msconvert-scripts

      Public
      Some shell scripts related to Thermo Fisher raw format conversion using msconvert
      Shell
      •
      Apache License 2.0
      •2•7•0•0•Updated Nov 18, 2024Nov 18, 2024

    • FragPipe

      Public
      A cross-platform proteomics data analysis suite
      guiproteomicsmass-spectrometrylabel-free-quantificationcommand-line-interfaceisobaric-quantificationdata-independent-acquisitiondata-dependent-acquisition
      Java
      •
      Other
      •38•205•58•2•Updated Nov 12, 2024Nov 12, 2024

    • philosopher

      Public
      PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
      gobioinformaticsdata-analysisproteomicsmass-spectrometryms-data
      Go
      •
      GNU General Public License v3.0
      •19•111•23•0•Updated Nov 12, 2024Nov 12, 2024

    • FragPipe-Analyst

      Public
      An easy-to-use and interactive web application for FragPipe
      1•5•10•0•Updated Nov 11, 2024Nov 11, 2024

    • FragPipe-PDV

      Public
      A forked PDV for FragPipe
      Java
      •
      GNU General Public License v3.0
      •20•1•0•0•Updated Oct 28, 2024Oct 28, 2024

    • pwiz

      Public
      The ProteoWizard Library is a set of software libraries and tools for rapid development of mass spectrometry and proteomic data analysis software.
      C#
      •
      Apache License 2.0
      •101•0•0•0•Updated Oct 26, 2024Oct 26, 2024

    • easypqp

      Public
      EasyPQP: Simple library generation for OpenSWATH
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •13•0•0•0•Updated Oct 15, 2024Oct 15, 2024

    • MSFragger-DDAPlus-Manuscript

      Public
      Python and R scripts to generate the figures in the MSFragger-DDA+ paper
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 14, 2024Oct 14, 2024

    • MSFragger-DIA-manuscript

      Public
      Python and R scripts to generate the figures in the MSFragger-DIA paper
      Python
      •
      Apache License 2.0
      •1•2•0•0•Updated Oct 14, 2024Oct 14, 2024

    • diaTracer-manuscript

      Public
      R
      •0•0•0•0•Updated Oct 10, 2024Oct 10, 2024

    • OpenMS

      Public
      The codebase of the OpenMS project
      C++
      •
      Other
      •318•0•0•0•Updated Oct 8, 2024Oct 8, 2024

    • MSBooster

      Public
      MSBooster allows users to add deep learning-based features to .pin files before Percolator PSM rescoring
      Java
      •
      GNU Lesser General Public License v3.0
      •2•16•1•0•Updated Oct 3, 2024Oct 3, 2024

    • PTM-Shepherd

      Public
      A tool for summarizing open search results
      Java
      •
      Apache License 2.0
      •5•14•0•0•Updated Sep 25, 2024Sep 25, 2024

    • FragPipeAnalystR

      Public
      R
      •
      GNU General Public License v3.0
      •1•4•4•0•Updated Sep 19, 2024Sep 19, 2024

    • OPair_FragPipe

      Public
      GDB
      •1•0•0•0•Updated Sep 13, 2024Sep 13, 2024

    • TMT-Integrator

      Public
      A tool integrates channel abundances from multiple TMT samples and exports a general report for downstream analysis.
      1•12•1•0•Updated Aug 9, 2024Aug 9, 2024

    • FragPipe-to-coADAPTr

      Public
      Standalone script to add FPOP/oxidative modifications column to FragPipe psm tables
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jul 25, 2024Jul 25, 2024

    • EntrapBench

      Public
      Generate entrapment database and calculate false discovery proportion (FDP)
      Java
      •
      Apache License 2.0
      •1•4•0•0•Updated Jul 17, 2024Jul 17, 2024

    • diaTracer

      Public
      A diaPASEF spectrum-centric analysis tool
      proteomicsdiadiapasef
      1•12•1•0•Updated Jul 3, 2024Jul 3, 2024

    • MSFragger

      Public
      Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
      bioinformaticsdatabase-searchproteomicsmass-spectrometry
      HTML
      •7•107•5•0•Updated Jun 20, 2024Jun 20, 2024

    • IonQuant

      Public
      A label free quantification tool.
      Other
      •8•16•7•0•Updated May 29, 2024May 29, 2024

    • FragPipeTPP

      Public
      Enables FragPipe Ouput from (TPP workflow) to be made compatible with TPP-R package
      R
      •
      Other
      •1•1•0•0•Updated May 10, 2024May 10, 2024

    • PD-Nodes

      Public
      The implementation of MSFragger and Philosopher (PeptideProphet) as Proteome Discoverer nodes
      1•8•4•0•Updated Apr 20, 2024Apr 20, 2024

    • Crystal-C

      Public
      Crystal-C: A computational tool for refinement of open search results
      Java
      •
      Apache License 2.0
      •3•5•2•0•Updated Apr 12, 2024Apr 12, 2024

    • sqlite-jdbc

      Public
      SQLite JDBC Driver
      Java
      •
      Apache License 2.0
      •619•0•0•0•Updated Mar 20, 2024Mar 20, 2024

    • timsrust

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •11•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • aho-corasick

      Public
      Java implementation of the Aho-Corasick algorithm for efficient string matching
      Java
      •
      Apache License 2.0
      •350•0•0•0•Updated Jan 23, 2024Jan 23, 2024

    • DIALib-QC

      Public
      DIALib-QC, an assessment tool for the systematic evaluation of spectral assay libraries to improve the data independent acquisition analysis.
      Perl
      •
      Other
      •2•0•0•0•Updated Dec 6, 2023Dec 6, 2023

    • picked_group_fdr

      Public
      Scalable, accurate and sensitive protein group FDRs for large-scale mass spectrometry experiments
      Jupyter Notebook
      •
      Apache License 2.0
      •5•0•0•0•Updated Dec 5, 2023Dec 5, 2023

    • alphapeptdeep

      Public
      Deep learning framework for proteomics
      Jupyter Notebook
      •
      Apache License 2.0
      •22•0•0•0•Updated Nov 13, 2023Nov 13, 2023