xcms - LC-MS and GC-MS Data Analysis

Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.

Last updated 24 days ago

immunooncologymassspectrometrymetabolomicsbioconductorfeature-detectionmass-spectrometrypeak-detection

14.35 score 185 stars 11 packages 832 scripts 3.3k downloads

mzR - parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry 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.

Last updated 3 days ago

immunooncologyinfrastructuredataimportproteomicsmetabolomicsmassspectrometry

12.62 score 42 stars 43 packages 188 scripts 5.6k downloads

CAMERA - Collection of annotation related methods for mass spectrometry data

Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments

Last updated 24 days ago

immunooncologymassspectrometrymetabolomics

10.37 score 11 stars 6 packages 163 scripts 804 downloads

Rdisop - Decomposition of Isotopic Patterns

In high resolution mass spectrometry (HR-MS), the measured masses can be decomposed into potential element combinations (chemical sum formulas). Where additional mass/intensity information of respective isotopic peaks is available, decomposition can take this information into account to better rank the potential candidate sum formulas. To compare measured mass/intensity information with the theoretical distribution of candidate sum formulas, the latter needs to be calculated. This package implements fast algorithms to address both tasks, the calculation of isotopic distributions for arbitrary sum formulas (assuming a HR-MS resolution of roughly 30,000), and the ranked list of sum formulas fitting an observed peak or isotopic peak set.

Last updated 4 days ago

immunooncologymassspectrometrymetabolomics

8.94 score 4 stars 2 packages 100 scripts 1.2k downloads