Alternatives and similar repositories for FragPipe-Analyst

Users that are interested in FragPipe-Analyst are comparing it to the libraries listed below

• cox-labs / CoxLab_Bug_Reporting

  View on GitHub
  MaxQuant and Perseus Bug Reporting
  ☆11Mar 19, 2025Updated 10 months ago
• Noble-Lab / Carafe

  View on GitHub
  High quality in silico spectral library generation for data-independent acquisition proteomics
  ☆16Nov 6, 2025Updated 3 months ago
• Nesvilab / diaTracer

  View on GitHub
  A diaPASEF spectrum-centric analysis tool
  ☆13Dec 24, 2025Updated last month
• mhoopmann / kojak

  View on GitHub
  Automatically exported from code.google.com/p/kojak-ms
  ☆13Apr 11, 2025Updated 10 months ago
• guoci / pycharm-smart-execute

  View on GitHub
  PyCharm plugin to execute python code
  ☆12Jul 29, 2025Updated 6 months ago
• Nesvilab / IonQuant

  View on GitHub
  A label free quantification tool.
  ☆18Jan 13, 2026Updated last month
• MonashProteomics / FragPipe-Analyst

  View on GitHub
  Documentation is available here:
  ☆25Dec 9, 2025Updated 2 months ago
• Nesvilab / MSBooster

  View on GitHub
  MSBooster allows users to add deep learning-based features to .pin files before Percolator PSM rescoring
  ☆21Updated this week
• Nesvilab / PTM-Shepherd

  View on GitHub
  A tool for summarizing open search results
  ☆16Dec 19, 2025Updated last month
• jingbo02 / Awesome-Denovo-Peptide-Sequencing

  View on GitHub
  Paper collection about de novo peptide Sequening
  ☆21Feb 5, 2025Updated last year
• CompOmics / ThermoRawFileParserGUI

  View on GitHub
  Graphical user interface for the ThermoRawFileParser
  ☆23Jul 5, 2024Updated last year
• Noble-Lab / cascadia

  View on GitHub
  Transformer deep learning model for de novo sequencing of data-independent acquisition mass spectrometry data
  ☆26Jan 27, 2026Updated 2 weeks ago
• wenbostar / PDV

  View on GitHub
  PDV: an integrative proteomics data viewer
  ☆60Feb 5, 2026Updated last week
• Nesvilab / FragPipe

  View on GitHub
  A cross-platform proteomics data analysis suite
  ☆276Updated this week
• snijderlab / stitch

  View on GitHub
  Template-based assembly of proteomics short reads for de novo antibody sequencing and repertoire profiling
  ☆28Oct 15, 2024Updated last year
• Roestlab / PythonProteomics

  View on GitHub
  A collection of available Python tools for Proteomics analysis
  ☆67Jan 31, 2026Updated last week
• snijderlab / annotator

  View on GitHub
  A simple tool to help you manually discover the depths of your (complex) spectra, one spectrum at a time.
  ☆33Feb 6, 2026Updated last week
• Nesvilab / philosopher

  View on GitHub
  PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
  ☆125Updated this week
• EliLillyCo / BioRels

  View on GitHub
  Biological Relationships - Biorels data preparation infrastructure for biology and drug discovery
  ☆14May 19, 2025Updated 8 months ago
• MonashBioinformaticsPlatform / LFQ-Analyst

  View on GitHub
  The repo for LFQ-Analyst
  ☆30Aug 7, 2024Updated last year
• vdemichev / DiaNN

  View on GitHub
  DIA-NN - a universal automated software suite for DIA proteomics data analysis.
  ☆421Feb 5, 2026Updated last week
• levitsky / pyteomics

  View on GitHub
  Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data. Pyteomics provi…
  ☆150Feb 5, 2026Updated last week
• broadinstitute / PANOPLY

  View on GitHub
  Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis C…
  ☆38Dec 17, 2025Updated last month
• Sika-Zheng-Lab / Shiba

  View on GitHub
  A versatile method for systematic identification of differential RNA splicing across platforms
  ☆15Jan 15, 2026Updated 3 weeks ago
• aws-samples / amazon-s3-checksum-tool

  View on GitHub
  ☆14Aug 16, 2024Updated last year
• kusterlab / picked_group_fdr

  View on GitHub
  Scalable, accurate and sensitive protein group FDRs for large-scale mass spectrometry experiments
  ☆13May 23, 2025Updated 8 months ago
• HUPO-PSI / psi-mod-CV

  View on GitHub
  PSI-MOD ontology for modified and unmodified amino acid residues
  ☆14Jan 8, 2026Updated last month
• MannLabs / DeepCollisionalCrossSection

  View on GitHub
  ☆10Mar 2, 2021Updated 4 years ago
• jasonwong-lab / LocusMasterTE

  View on GitHub
  Integrating long read sequencing enhances short read-based locus-specific transposable element quantification
  ☆10May 12, 2025Updated 9 months ago
• rvaldes / IPHOMED

  View on GitHub
  IPHOMED
  ☆11Jun 11, 2025Updated 8 months ago
• ProGenNo / ProHap

  View on GitHub
  Proteogenomics database-generation tool for protein haplotypes and variants
  ☆11Jun 19, 2025Updated 7 months ago
• HUPO-PSI / mzTab

  View on GitHub
  mzTab Reporting MS-based Proteomics and Metabolomics Results
  ☆45Apr 1, 2025Updated 10 months ago
• PulverCyril / craTEs

  View on GitHub
  Estimate the cis-regulatory activity of transposable element (TEs) subfamilies
  ☆10Dec 15, 2023Updated 2 years ago
• ag-warscheid / autoprot

  View on GitHub
  autoprot provides standardised, fast, and reliable proteomics data analysis while ensuring a high customisability needed to tailor the an…
  ☆10Jan 28, 2026Updated 2 weeks ago
• sgibb / cleaver

  View on GitHub
  Cleavage of polypeptide sequences
  ☆12Oct 14, 2025Updated 3 months ago
• MPUSP / snakemake-ms-proteomics

  View on GitHub
  Pipeline for automatic processing and quality control of mass spectrometry data
  ☆13Jan 30, 2025Updated last year
• czbiohub-sf / protdata

  View on GitHub
  Dataloader for common proteomics search engine outputs into AnnData format
  ☆14Nov 24, 2025Updated 2 months ago
• karakulahg / TEffectR

  View on GitHub
  ☆10Jan 29, 2020Updated 6 years ago
• Hoffmann-Lab / TEdetectionEvaluation

  View on GitHub
  Tool comparison for detecting differentially expressed individual transposable elements
  ☆11Jan 7, 2022Updated 4 years ago