topdownr

Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.

MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.

mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.

A client to simplify fetching predictions from the Koina web service. Koina is a model repository enabling the remote execution of models. Predictions are generated as a response to HTTP/S requests, the standard protocol used for nearly all web traffic.

The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.

The PSMatch package helps proteomics practitioners to load, handle and manage Peptide Spectrum Matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions.