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@Nesvilab

Nesvilab

Alexey Nesvizhskii's proteome bioinformatics group.

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  1. FragPipe FragPipe Public

    A cross-platform proteomics data analysis suite

    Java 216 40

  2. MSFragger MSFragger Public

    Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

    HTML 110 7

  3. MSBooster MSBooster Public

    MSBooster allows users to add deep learning-based features to .pin files before Percolator PSM rescoring

    Java 16 2

  4. philosopher philosopher Public

    PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering

    Go 114 19

  5. PTM-Shepherd PTM-Shepherd Public

    A tool for summarizing open search results

    Java 15 5

  6. IonQuant IonQuant Public

    A label free quantification tool.

    16 8

Repositories

Showing 10 of 43 repositories
  • FragPipe Public

    A cross-platform proteomics data analysis suite

    Nesvilab/FragPipe’s past year of commit activity
    Java 216 40 59 2 Updated Jan 25, 2025
  • MSBooster Public

    MSBooster allows users to add deep learning-based features to .pin files before Percolator PSM rescoring

    Nesvilab/MSBooster’s past year of commit activity
    Java 16 LGPL-3.0 2 0 0 Updated Jan 24, 2025
  • ProteoBench Public Forked from Proteobench/ProteoBench

    ProteoBench is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. Our goal is to allow a continuous, easy, and controlled comparison of proteomics data analysis workflows. https://proteobench.cubimed.rub.de/

    Nesvilab/ProteoBench’s past year of commit activity
    Jupyter Notebook 0 Apache-2.0 12 0 0 Updated Jan 24, 2025
  • PIP-ECHOanalysis Public Forked from Alexander-Sol/PIP-ECHOanalysis

    A repository accompanying the manuscript "Improved detection of differentially abundant proteins through FDR-control of peptide-identity-propagation"

    Nesvilab/PIP-ECHOanalysis’s past year of commit activity
    Jupyter Notebook 0 MIT 1 0 0 Updated Jan 23, 2025
  • easypqp Public Forked from grosenberger/easypqp

    EasyPQP: Simple library generation for OpenSWATH

    Nesvilab/easypqp’s past year of commit activity
    Python 0 BSD-3-Clause 14 0 0 Updated Jan 17, 2025
  • FragPipe-to-coADAPTr Public

    Standalone script to add FPOP/oxidative modifications column to FragPipe psm tables

    Nesvilab/FragPipe-to-coADAPTr’s past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated Jan 8, 2025
  • MSFragger-DDAPlus-Manuscript Public

    Python and R scripts to generate the figures in the MSFragger-DDA+ paper

    Nesvilab/MSFragger-DDAPlus-Manuscript’s past year of commit activity
    Jupyter Notebook 0 Apache-2.0 0 0 0 Updated Dec 23, 2024
  • philosopher Public

    PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering

    Nesvilab/philosopher’s past year of commit activity
    Go 114 GPL-3.0 19 26 (1 issue needs help) 0 Updated Dec 22, 2024
  • FragPipeAnalystR Public
    Nesvilab/FragPipeAnalystR’s past year of commit activity
    R 4 GPL-3.0 2 8 1 Updated Dec 19, 2024
  • PTM-Shepherd Public

    A tool for summarizing open search results

    Nesvilab/PTM-Shepherd’s past year of commit activity
    Java 15 Apache-2.0 5 0 0 Updated Dec 16, 2024
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