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Nesvilab's Projects

aho-corasick icon aho-corasick

Java implementation of the Aho-Corasick algorithm for efficient string matching

batmass icon batmass

Mass spectrometry data visualization

clean-storage icon clean-storage

A shell script to clean the Storage. Internal use only. DISCLAIMER: not responsible for loss of data.

crystal-c icon crystal-c

Crystal-C: A computational tool for refinement of open search results

deltamass icon deltamass

DeltaMass: view and interrogate open proteomics search data

dia-umpire icon dia-umpire

Computational analysis for mass spectrometry-based proteomics data

dialib-qc icon dialib-qc

DIALib-QC, an assessment tool for the systematic evaluation of spectral assay libraries to improve the data independent acquisition analysis.

easypqp icon easypqp

EasyPQP: Simple library generation for OpenSWATH

entrapbench icon entrapbench

Generate entrapment database and calculate false discovery proportion (FDP)

fragpipe icon fragpipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data

fragpipetpp icon fragpipetpp

Enables FragPipe Ouput from (TPP workflow) to be made compatible with TPP-R package

libmatic icon libmatic

DIA-Umpire based pipeline for generation of spectral libraries for targeted analysis of DIA data.

lucxor icon lucxor

JAVA-based implementation of LuciPHOr that can process any variable PTM.

msbooster icon msbooster

MSBooster allows users to add deep learning-based features to .pin files before Percolator PSM rescoring

msfragger icon msfragger

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

msftbx icon msftbx

MS File ToolBox - tools for parsing some mass-spectrometry related file formats (mzML, mzXML, pep.xml, prot.xml, etc.)

pd-nodes icon pd-nodes

The implementation of MSFragger and Philosopher (PeptideProphet) as Proteome Discoverer nodes

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