Base Classes and Functions for Mass Spectrometry and Proteomics
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Updated
May 15, 2024 - R
Base Classes and Functions for Mass Spectrometry and Proteomics
Using R and Bioconductor packages for the analysis and comprehension of proteomics data.
Ursgal - universal Python module combining common bottom-up proteomics tools for large-scale analysis
Library for mass spectrometry projects
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.
A unifying bioinformatics framework for organelle proteomics
An exploration of internal reference scaling (IRS) normalization in isobaric tagging proteomics experiments.
Examples of TMT data analyses using R. Links to notebooks and repositories. Also a few spectral counting analyses.
ProXI: Schema definitions for the Proteomics eXpression Interface
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).
DeltaMass: view and interrogate open proteomics search data
Custom analysis of in vitro circadian proteomics and phosphoproteomics using multiple sets of 10plex TMT with two genotypes
PACOM (Proteomics Assay COMparator) is a Java stand alone tool for visualize and compare large proteomics datasets
Simple workflows for the isobaric-labeling proteomic data from Proteome Discoverer with ANOVA, t-testing, DEqMS/limma and annotation via fgsea
Converter from Census TMT output file to the input of MSstatsTMT
List of online databases and resources for Mycobacterium Tuberculosis
General Java util classes used across different projects
Feature extraction from .pdb files
MaxQuant and Perseus Bug Reporting
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