Computational Omics and Systems Biology Group
The CompOmics group, headed by Prof. Dr. Lennart Martens, specializes in the management, analysis and integration of high-throughput Omics data.
Pinned Repositories
compomics-utilities
Open source Java library for computational proteomics
DeepLC
DeepLC: Retention time prediction for (modified) peptides using Deep Learning.
meta-proteome-analyzer
MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.
moFF
A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file
ms2pip
MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
ms2rescore
Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
peptide-shaker
Interpretation of proteomics identification results
psm_utils
Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
searchgui
Highly adaptable common interface for proteomics search and de novo engines
ThermoRawFileParser
Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono
Computational Omics and Systems Biology Group's Repositories
compomics/spectrum_similarity
Scoring functions to compare MS/MS spectra
compomics/pladipus
Platform for Distributed Proteomics Software
compomics/xilmass
An algorithm to identify cross-linked peptides
compomics/CellMojo
compomics/dbtoolkit
Manipulating fasta sequence databases
compomics/ReSpinOnline
Online public viewer for ReSpin Results
compomics/search-all-assess-subset
An implementation of the Search All, Asses Subset strategy for FDR estimation in shotgun proteomics.
compomics/spectrawl
A rich client tool used for browsing through spectra looking for specific mass differences.
compomics/compomics-crowd
Library that allows for windows users to contribute to science through donating cpu cycles behind a screensaver
compomics/cell-motility
Enabling the analysis of cell motility paths over time.
compomics/cluster-data-generation
Filter and export spectrum from PRIDE Archive
compomics/commons
compomics/compomics-ensh
Java hibernate model for ensembl.
compomics/compomics-sigpep
Predicting peptide signatures for targeted proteomics.
compomics/COSS-Archive-
CompOmics Spectral Similarity Search Tool
compomics/icelogoserver
The server edition of the iceLogo tool.
compomics/ipython-notebook-server
Mini tornado server to provide multiple iPython notebook kernels from a single machine.
compomics/jwrapper-pepnovo
compomics/LFQ_galaxy_p
Enable protein summarisation and quantitation in Galaxy-P
compomics/Lorikeet_spectrum_viewer
Python script to annotate MS2 spectra from MHGF file.
compomics/MAPPI-DAT
analysis and data management tool for high-throughput protein-protein interaction data generated from microarray-MAPPIT system
compomics/mslimsdatfileextractor
simple jar for extracting dat files from mslims projects
compomics/oxPTMScanner
compomics/PeptideMapper-Benchmark
Benchmark dataset for PeptideMapper paper.
compomics/ProteinAssociationPair
compomics/psi_io
compomics/search-all-assess-subset-paper
compomics/toppr
The Online Protein Processing Resource.
compomics/visualisationtool
visualisation tool for proteins
compomics/xltools