Alternatives and similar repositories for PDV

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

• IFIproteomics / LFQbench
  ☆24Updated 2 years ago
• 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 month
• bigbio / quantms
  Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Iso…
  ☆64Updated this week
• Vitek-Lab / MSstats
  R package - MSstats
  ☆87Updated last month
• jessegmeyerlab / proteomics-tutorial
  ☆66Updated last year
• Nesvilab / philosopher
  PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
  ☆120Updated this week
• vdemichev / diann-rpackage
  Report processing and protein quantification for MS-based proteomics
  ☆50Updated 2 years ago
• bigbio / proteomics-sample-metadata
  The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets
  ☆98Updated 2 months ago
• Nesvilab / MSFragger
  Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
  ☆122Updated 5 months ago
• UWPR / Comet
  An tandem mass spectrometry (MS/MS) sequence database search tool.
  ☆53Updated last week
• MannLabs / directlfq
  Fast and accurate label-free quantification for small and very large numbers of proteomes
  ☆60Updated 3 weeks ago
• fgcz / prolfqua
  Differential Expression Analysis tool box R lang package for omics data
  ☆46Updated last month
• ftwkoopmans / msdap
  MS-DAP: downstream analysis pipeline for quantitative proteomics
  ☆40Updated 9 months ago
• tvpham / iq
  An R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
  ☆32Updated last month
• wfondrie / mokapot
  Fast and flexible semi-supervised learning for peptide detection in Python
  ☆49Updated 9 months ago
• MonashBioinformaticsPlatform / LFQ-Analyst
  The repo for LFQ-Analyst
  ☆30Updated last year
• MannLabs / alphamap
  An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.
  ☆89Updated 3 weeks ago
• cbielow / PTXQC
  A Quality Control (QC) pipeline for Proteomics (PTX) results generated by MaxQuant
  ☆47Updated 4 months ago
• MannLabs / ProteomicsVisualization
  This is a collection of minimal code to visualize various aspects of proteomics data.
  ☆82Updated 3 years ago
• cox-labs / CoxLab_Bug_Reporting
  MaxQuant and Perseus Bug Reporting
  ☆10Updated 8 months ago
• RASpicer / MetabolomicsTools
  ☆55Updated 4 years ago
• statisticalbiotechnology / triqler
  The triqler (TRansparent Identification-Quantification-linked Error Rates)'s source and example code
  ☆24Updated 2 months ago
• smith-chem-wisc / MetaMorpheus
  Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
  ☆104Updated 2 weeks ago
• bigbio / pmultiqc
  A library for QC report based on MultiQC framework
  ☆22Updated last week
• MonashProteomics / FragPipe-Analyst
  Documentation is available here:
  ☆20Updated last week
• PRIDE-Archive / pridepy
  Python client for PRIDE Archive Rest API.
  ☆26Updated last month
• broadinstitute / PANOPLY
  Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis C…
  ☆37Updated 3 weeks ago
• Proteobench / ProteoBench
  ProteoBench is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. Our goal is to…
  ☆49Updated this week
• pwilmart / PAW_pipeline
  A Comet-based, best practices proteomics pipeline.
  ☆39Updated last year
• ComputationalProteomics / NormalyzerDE
  Tools for normalization, evaluation of outliers, technical biases and batch effects and differential expression analysis.
  ☆25Updated 5 months ago