Alternatives and similar repositories for PepNet

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

• MSGFPlus / msgfplus
  MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence …
  ☆81Updated last year
• denisbeslic / denovopipeline
  Pipeline for de novo peptide sequencing (Novor, DeepNovo, SMSNet, PointNovo, Casanovo) and assembly with ALPS.
  ☆42Updated last year
• wfondrie / mokapot
  Fast and flexible semi-supervised learning for peptide detection in Python
  ☆48Updated 7 months ago
• MannLabs / alphamap
  An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.
  ☆86Updated last month
• MannLabs / alphapeptdeep
  Deep learning framework for proteomics
  ☆132Updated last month
• UWPR / Comet
  An tandem mass spectrometry (MS/MS) sequence database search tool.
  ☆54Updated this week
• bigbio / quantms
  Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Iso…
  ☆57Updated 3 weeks ago
• bzhanglab / deep_learning_in_proteomics
  A list of tools on proteomics using deep learning
  ☆106Updated last year
• Nesvilab / MSFragger
  Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
  ☆121Updated 3 months ago
• CompOmics / ms2pip
  MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
  ☆46Updated 6 months ago
• CompOmics / DeepLC
  DeepLC: Retention time prediction for (modified) peptides using Deep Learning.
  ☆70Updated 2 weeks ago
• wilhelm-lab / oktoberfest
  Rescoring and spectral library generation pipeline for proteomics.
  ☆49Updated last week
• ProteomicsML / ProteomicsML
  Community-curated tutorials and datasets for ML in proteomics
  ☆55Updated last month
• wenbostar / PDV
  PDV: an integrative proteomics data viewer
  ☆55Updated 2 months ago
• MannLabs / alphaviz
  AlphaViz is a cutting-edge browser-based interactive visualization tool allowing to visualize the processed mass spectrometry data acquir…
  ☆34Updated 5 months ago
• pFindStudio / pDeep3
  MS/MS prediction for peptides
  ☆24Updated 4 years ago
• kusterlab / prosit
  Prosit offers high quality MS2 predicted spectra for any organism and protease as well as iRT prediction. When using Prosit is helpful fo…
  ☆89Updated 2 years ago
• nh2tran / DeepNovo-DIA
  De novo peptide sequencing for DDA and DIA by deep learning
  ☆36Updated 4 years ago
• Nesvilab / MSBooster
  MSBooster allows users to add deep learning-based features to .pin files before Percolator PSM rescoring
  ☆19Updated this week
• wilhelm-lab / koina
  Democratizing ML in proteomics
  ☆43Updated last month
• tvpham / iq
  An R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
  ☆31Updated 7 months ago
• jessegmeyerlab / proteomics-tutorial
  ☆65Updated last year
• MannLabs / ProteomicsVisualization
  This is a collection of minimal code to visualize various aspects of proteomics data.
  ☆83Updated 3 years ago
• LiChenPU / NetID
  A global network optimization approach for untargeted LC-MS metabolomics data annotation and metabolite discovery
  ☆47Updated 2 years ago
• MatteoLacki / timsr
  TimsR: Easy access to timsTOF Pro data from R.
  ☆12Updated 4 years ago
• Nesvilab / philosopher
  PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
  ☆118Updated 2 weeks ago
• MannLabs / directlfq
  Fast and accurate label-free quantification for small and very large numbers of proteomes
  ☆60Updated last month
• 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 this week
• CompOmics / ms2rescore
  Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
  ☆62Updated this week