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enviGCMS - GC/LC-MS Data Analysis for Environmental Science

Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.

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environmentmass-spectrometrymetabolomics

6.61 score 18 stars 2 dependents 38 scripts 227 downloads

pmd - Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted Analysis and Reactomics Analysis

Paired mass distance (PMD) analysis proposed in Yu, Olkowicz and Pawliszyn (2018) <doi:10.1016/j.aca.2018.10.062> and PMD based reactomics analysis proposed in Yu and Petrick (2020) <doi:10.1038/s42004-020-00403-z> for gas/liquid chromatography–mass spectrometry (GC/LC-MS) based non-targeted analysis. PMD analysis including GlobalStd algorithm and structure/reaction directed analysis. GlobalStd algorithm could found independent peaks in m/z-retention time profiles based on retention time hierarchical cluster analysis and frequency analysis of paired mass distances within retention time groups. Structure directed analysis could be used to find potential relationship among those independent peaks in different retention time groups based on frequency of paired mass distances. Reactomics analysis could also be performed to build PMD network, assign sources and make biomarker reaction discovery. GUIs for PMD analysis is also included as 'shiny' applications.

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mass-spectrometrymetabolomicsnon-target

6.16 score 11 stars 44 scripts 241 downloads

sfi - Data analysis for Single File Injections (SFIs) mode LC-MS analysis

Data analysis for Single File Injections(SFIs) mode LC-MS analysis. In SFIs mode, pooled samples are initially injected to serve as reference peaks for subsequent analyses. Repeated injections of individual samples are then performed at fixed time intervals using isocratic elution. This package provides the functions to analyze data from SFIs mode including peak picking and peak reassignment.

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massspectrometrymetabolomicsfeatureextractioncpp

4.78 score 1 stars 5 scripts 201 downloads

rgabriel - Gabriel Multiple Comparison Test and Plot the Confidence Interval on Barplot

Analyze multi-level one-way experimental designs where there are unequal sample sizes and population variance homogeneity can not be assumed. To conduct the Gabriel test <doi:10.2307/2286265>, create two vectors: one for your observations and one for the factor level of each observation. The function, rgabriel, conduct the test and save the output as a vector to input into the gabriel.plot function, which produces a confidence interval plot for Multiple Comparison.

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2.70 score 1 stars 4 scripts 188 downloads