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High level functionality to support and simplify metabolomics data annotation.
A Thermo XCalibur Method (.meth) file reader, extracter, and converter command-line program for mass spectrometry researchers.
Proteomics search & quantification so fast that it feels like magic
Comparing glycoprofiles, leveraging motif substructure arithmetic
R package for calculation and mass spectrometry annotation of glycans
The ProteoWizard Library is a set of software libraries and tools for rapid development of mass spectrometry and proteomic data analysis software.
GlyCombo, a combinatorial glycan composition assignment tool
A library for deisotoping and charge state deconvolution of complex mass spectra
An LC-MS/MS glycan and glycopeptide search engine
Glycan Analysis and Glycoinformatics Library for Python
Predicting glycan structure from LC-MS/MS data
Package for processing and analyzing glycans and their role in biology.
The repository for Targeted Feature Detection and Extraction (TFD/E).
Spectra backend supporting TimsTOF data files using the opentimsr package.
MannLabs / Quality-Control-of-the-Plasma-Proteome
Forked from EugeniaVoytik/Quality-Control-of-the-Plasma-ProteomeAn open-source Python package for efficient accession and visualization of Bruker TimsTOF raw data from the Mann Labs at the Max Planck Institute of Biochemistry.
Construction, quantification, and visualization of proteoform families
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
This is a R package for alignment of DIA mass-spec data
Python package for efficient mass spectrometry data processing and visualization
TopPIC suite is a software suite for proteoform identification by top-down mass spectrometry.
R package for processing results from TopPIC, including resolving ambiguity in proteoform identification
Use open search results (from Morpheus) to create a database with uncovered candidate PTM annotations
Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)