A cross-platform proteomics data analysis suite
Proteomics label-free quantification (LFQ) analysis pipeline
Protein Cluster Quant is a Java software for the analysis of complex proteomics samples (quantitative or not). It helps to reduce the redundancy of the peptide-to-protein relationship and to visualize the results in a bipartite network (Cytoscape).
CellLocator: Automated live-cell image analysis for Incucyte®. Streamlined cell segmentation, fluorescence quantification, and kinetic analysis. Open-source and freely available under the MIT License.
Parser for quantitative data from files created by Census software.
R package that visualizes MaxQuant output of activity-based protein profiling experiments.
Missing-value imputation benchmark for peptide-level LFQ proteomics. Evaluated on a spike-in dataset and via simulation.
Label-free DDA proteomics differential abundance analysis, benchmarked against a spike-in study with known ground truth and applied to an arginine transporter knockout in Francisella tularensis.
End to end command line proteomics, Thermo RAW files through Sage search and label-free quantification to differential abundance, with entrapment-based validation of the reported false discovery rate.
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