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Kevin Kovalchik's Projects

chopper icon chopper

A simple tool for chopping up FASTA files.

my_prosit icon my_prosit

Prosit offers high quality MS2 predicted spectra for any organism and protease as well as iRT prediction. When using Prosit is helpful for your research, please cite "Gessulat, Schmidt et al. 2019" DOI 10.1038/s41592-019-0426-7

plotly-logo icon plotly-logo

A Python library for making amino acid sequence logos using the Plotly framework.

proteotools icon proteotools

A simple Python package which lets you programmatically run a few proteomics search engines (Comet, X! Tandem, MS-GF+) and use compiled Trans-Proteomic Pipeline (TPP) binaries without needing to compile the entire pipeline.

pynetmhcpan icon pynetmhcpan

A simple tool for using NetMHCpan and NetMHCIIpan using multiple CPUs in a Python environment.

rawquant icon rawquant

RawQuant is a Python package for extracting scan meta data and quantification values from Thermo .raw files.

rawtools icon rawtools

RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files from data-dependent acquisition experiments.

realtimeorbiwiz icon realtimeorbiwiz

An application for testing access to Orbitrap RAW files during acquisition.

unspecific-decoy-generator icon unspecific-decoy-generator

A tool for generating decoy proteins sequences for use with mass pectrometry database searches, specifically intended for unspecific digest searches.

upsetplotly icon upsetplotly

A Python package for creating UpSet plots using the Plotly framework

x-tandem-for-centos icon x-tandem-for-centos

A verbatim clone of X! Tandem, version Alanine, but with release builds compiled in CentOS 7.

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