Pinned Repositories
DIA-Umpire
Computational analysis for mass spectrometry-based proteomics data
diaTracer
A diaPASEF spectrum-centric analysis tool
FragPipe
A cross-platform proteomics data analysis suite
IonQuant
A label free quantification tool.
MSBooster
MSBooster allows users to add deep learning-based features to .pin files before Percolator PSM rescoring
MSFragger
Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
PD-Nodes
The implementation of MSFragger and Philosopher (PeptideProphet) as Proteome Discoverer nodes
philosopher
PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
PTM-Shepherd
A tool for summarizing open search results
TMT-Integrator
A tool integrates channel abundances from multiple TMT samples and exports a general report for downstream analysis.
Nesvilab's Repositories
Nesvilab/FragPipe
A cross-platform proteomics data analysis suite
Nesvilab/philosopher
PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
Nesvilab/MSFragger
Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
Nesvilab/MSBooster
MSBooster allows users to add deep learning-based features to .pin files before Percolator PSM rescoring
Nesvilab/IonQuant
A label free quantification tool.
Nesvilab/PTM-Shepherd
A tool for summarizing open search results
Nesvilab/diaTracer
A diaPASEF spectrum-centric analysis tool
Nesvilab/TMT-Integrator
A tool integrates channel abundances from multiple TMT samples and exports a general report for downstream analysis.
Nesvilab/PD-Nodes
The implementation of MSFragger and Philosopher (PeptideProphet) as Proteome Discoverer nodes
Nesvilab/FragPipe-Analyst
An easy-to-use and interactive web application for FragPipe
Nesvilab/msconvert-scripts
Some shell scripts related to Thermo Fisher raw format conversion using msconvert
Nesvilab/Crystal-C
Crystal-C: A computational tool for refinement of open search results
Nesvilab/FragPipeAnalystR
Nesvilab/EntrapBench
Generate entrapment database and calculate false discovery proportion (FDP)
Nesvilab/MSFragger-DIA-manuscript
Python and R scripts to generate the figures in the MSFragger-DIA paper
Nesvilab/FragPipe-PDV
A forked PDV for FragPipe
Nesvilab/FragPipeTPP
Enables FragPipe Ouput from (TPP workflow) to be made compatible with TPP-R package
Nesvilab/FragPipe-to-coADAPTr
Standalone script to add FPOP/oxidative modifications column to FragPipe psm tables
Nesvilab/alphapeptdeep
Deep learning framework for proteomics
Nesvilab/diaTracer-manuscript
Nesvilab/easypqp
EasyPQP: Simple library generation for OpenSWATH
Nesvilab/MSFragger-DDAPlus-Manuscript
Python and R scripts to generate the figures in the MSFragger-DDA+ paper
Nesvilab/OPair_FragPipe
Nesvilab/OpenMS
The codebase of the OpenMS project
Nesvilab/PepCentric-manuscript
Scripts to generate the results in the PepCentric paper
Nesvilab/PIP-ECHOanalysis
A repository accompanying the manuscript "Improved detection of differentially abundant proteins through FDR-control of peptide-identity-propagation"
Nesvilab/ProteoBench
ProteoBench is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. Our goal is to allow a continuous, easy, and controlled comparison of proteomics data analysis workflows. https://proteobench.cubimed.rub.de/
Nesvilab/pwiz
The ProteoWizard Library is a set of software libraries and tools for rapid development of mass spectrometry and proteomic data analysis software.
Nesvilab/sqlite-jdbc
SQLite JDBC Driver
Nesvilab/timsrust