Alternatives and similar repositories for ProteoBench:

Users that are interested in ProteoBench are comparing it to the libraries listed below

• wilhelm-lab / koina
  Democratizing ML in proteomics
  ☆34Updated last week
• wfondrie / mokapot
  Fast and flexible semi-supervised learning for peptide detection in Python
  ☆43Updated 2 months ago
• wilhelm-lab / oktoberfest
  Rescoring and spectral library generation pipeline for proteomics.
  ☆37Updated 2 weeks ago
• MannLabs / timsrust
  ☆25Updated 2 weeks ago
• MannLabs / directlfq
  Fast and accurate label-free quantification for small and very large numbers of proteomes
  ☆44Updated this week
• gtluu / timsconvert
  ☆35Updated 3 weeks ago
• UWPR / Comet
  An tandem mass spectrometry (MS/MS) sequence database search tool.
  ☆47Updated this week
• compomics / DeepLC
  DeepLC: Retention time prediction for (modified) peptides using Deep Learning.
  ☆58Updated 2 weeks ago
• statisticalbiotechnology / maracluster
  Matthew The's implementation of MaRaCluster
  ☆11Updated 2 years ago
• Villen-Lab / pyAscore
  A python package for fast post translational modification localization, powered by Cython.
  ☆18Updated last year
• MannLabs / alphamap
  An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.
  ☆79Updated this week
• Nesvilab / diaTracer
  A diaPASEF spectrum-centric analysis tool
  ☆12Updated 7 months ago
• compomics / psm_utils
  Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
  ☆26Updated last month
• MannLabs / alphadia
  modular & open DIA search
  ☆60Updated this week
• thermofisherlsms / iapi
  Instrument Application Programming Interface
  ☆45Updated last week
• theGreatHerrLebert / sagepy
  A python interface to the SAGE search engine for mass spectrometry proteomics
  ☆11Updated this week
• MannLabs / alphapeptdeep
  Deep learning framework for proteomics
  ☆116Updated this week
• ProteomicsML / ProteomicsML
  Community-curated tutorials and datasets for ML in proteomics
  ☆49Updated 2 months ago
• MannLabs / alphatims
  An open-source Python package for efficient accession and visualization of Bruker TimsTOF raw data from the Mann Labs at the Max Planck I…
  ☆84Updated 2 months ago
• statisticalbiotechnology / diffacto
  ☆13Updated 11 months ago
• Protea-Glycosciences / GlyCombo
  GlyCombo, a combinatorial glycan composition assignment tool
  ☆12Updated this week
• compomics / ms2pip
  MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
  ☆40Updated 3 weeks ago
• mafreitas / tdf2mzml
  ☆25Updated last year
• MannLabs / ProteomicsVisualization
  This is a collection of minimal code to visualize various aspects of proteomics data.
  ☆71Updated 3 years ago
• MannLabs / structuremap
  Python package for investigating the structural context of PTMs
  ☆28Updated last month
• rusteomics / mzcore
  A Rust library for parsing ProForma peptides and matching them against MS spectra, formally known as rustyms
  ☆24Updated this week
• wilhelm-lab / PROSPECT
  Proteomics Mass Spectrometry Datasets for Machine Learning
  ☆13Updated 6 months ago
• bigbio / proteomics-sample-metadata
  The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets
  ☆80Updated 4 months ago
• tvpham / iq
  An R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
  ☆24Updated 2 months ago
• michalsta / opentims
  Open-source C++ and Python module for opening binary timsTOF data files.
  ☆45Updated 2 months ago