Alternatives and similar repositories for PTM-Shepherd

Users that are interested in PTM-Shepherd are comparing it to the libraries listed below

• UWPR / Comet
  An tandem mass spectrometry (MS/MS) sequence database search tool.
  ☆54Updated this week
• wilhelm-lab / oktoberfest
  Rescoring and spectral library generation pipeline for proteomics.
  ☆50Updated this week
• smith-chem-wisc / FlashLFQ
  Ultra-fast label-free quantification algorithm for mass-spectrometry proteomics
  ☆22Updated 3 months ago
• Nesvilab / MSFragger
  Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
  ☆121Updated 4 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…
  ☆90Updated 2 months ago
• Proteobench / ProteoBench
  ProteoBench is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. Our goal is to…
  ☆48Updated this week
• tvpham / iq
  An R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
  ☆31Updated 2 weeks ago
• MannLabs / alphamap
  An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.
  ☆86Updated 2 months ago
• statisticalbiotechnology / triqler
  The triqler (TRansparent Identification-Quantification-linked Error Rates)'s source and example code
  ☆24Updated last month
• kevinkovalchik / RawTools
  RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control ana…
  ☆65Updated 2 years ago
• MannLabs / directlfq
  Fast and accurate label-free quantification for small and very large numbers of proteomes
  ☆60Updated 2 months ago
• wilhelm-lab / koina
  Democratizing ML in proteomics
  ☆44Updated 2 months ago
• CompOmics / ms2rescore
  Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
  ☆61Updated last week
• bigbio / proteomics-sample-metadata
  The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets
  ☆96Updated last month
• CompOmics / ms2pip
  MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
  ☆47Updated 7 months ago
• thermofisherlsms / RawFileReader
  ☆63Updated 7 months ago
• wfondrie / mokapot
  Fast and flexible semi-supervised learning for peptide detection in Python
  ☆48Updated 8 months ago
• thermofisherlsms / iapi
  Instrument Application Programming Interface
  ☆51Updated last month
• gtluu / timsconvert
  ☆42Updated 7 months ago
• mafreitas / tdf2mzml
  ☆27Updated 2 years ago
• wenbostar / PDV
  PDV: an integrative proteomics data viewer
  ☆57Updated 3 months ago
• CompOmics / ThermoRawFileParser
  Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono
  ☆226Updated last week
• statisticalbiotechnology / diffacto
  ☆13Updated last year
• michalsta / opentims
  Open-source C++ and Python module for opening binary timsTOF data files.
  ☆49Updated 4 months ago
• IFIproteomics / LFQbench
  ☆24Updated 2 years ago
• smith-chem-wisc / MetaMorpheus
  Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
  ☆102Updated last week
• MannLabs / alphapeptdeep
  Deep learning framework for proteomics
  ☆132Updated last month
• MannLabs / alphadia
  modular & open DIA search
  ☆80Updated last week
• Protea-Glycosciences / GlyCombo
  GlyCombo, a combinatorial glycan composition assignment tool
  ☆12Updated 8 months ago
• vdemichev / diann-rpackage
  Report processing and protein quantification for MS-based proteomics
  ☆49Updated 2 years ago