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patRoon - Workflows for Mass-Spectrometry Based Non-Target Analysis

Provides an easy-to-use interface to a mass spectrometry based non-target analysis workflow. Various (open-source) tools are combined which provide algorithms for extraction and grouping of features, extraction of MS and MS/MS data, automatic formula and compound annotation and grouping related features to components. In addition, various tools are provided for e.g. data preparation and cleanup, plotting results and automatic reporting.

Last updated

mass-spectrometrynon-targetzlibcppopenmpopenjdk

6.86 score 79 stars 117 scripts

qlcMatrix - Utility Sparse Matrix Functions for Quantitative Language Comparison

Extension of the functionality of the 'Matrix' package for using sparse matrices. Some of the functions are very general, while other are highly specific for special data format as used for quantitative language comparison.

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6.70 score 6 stars 1 dependents 310 scripts 1.8k downloads

RAMClustR - Mass Spectrometry Metabolomics Feature Clustering and Interpretation

A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. This method is compatible with gas and liquid chromatography coupled mass spectrometry, including indiscriminant tandem mass spectrometry data <DOI: 10.1021/ac501530d>.

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massspectrometrymetabolomics

6.11 score 13 stars 25 scripts 53 downloads

splashR - splashR - package to create hashes for spectra

This package allows the calculation of spectral hashes.

Last updated

5.28 score 26 stars 61 scripts

RDCOMClient - R-DCOM client

Provides dynamic client-side access to (D)COM applications from within R.

Last updated

4.07 score 465 scripts

fastAdaboost - a Fast Implementation of Adaboost

Implements Adaboost based on C++ backend code. This is blazingly fast and especially useful for large, in memory data sets. The package uses decision trees as weak classifiers. Once the classifiers have been trained, they can be used to predict new data. Currently, we support only binary classification tasks. The package implements the Adaboost.M1 algorithm and the real Adaboost(SAMME.R) algorithm.

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cpp

3.93 score 11 stars 156 scripts 14 downloads

cliqueMS - Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data

Annotates data from liquid chromatography coupled to mass spectrometry (LC/MS) metabolomics experiments. Based on a network algorithm (O.Senan, A. Aguilar- Mogas, M. Navarro, O. Yanes, R.Guimerà and M. Sales-Pardo, Bioinformatics, 35(20), 2019), 'CliqueMS' builds a weighted similarity network where nodes are features and edges are weighted according to the similarity of this features. Then it searches for the most plausible division of the similarity network into cliques (fully connected components). Finally it annotates metabolites within each clique, obtaining for each annotated metabolite the neutral mass and their features, corresponding to isotopes, ionization adducts and fragmentation adducts of that metabolite.

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metabolomicsmassspectrometrynetworknetworkinferencecpp

3.75 score 28 scripts 1 downloads

MetaClean - Detection of Low-Quality Peaks in Untargeted Metabolomics Data

Utilizes 11 peak quality metrics and 8 diverse machine learning algorithms to build a classifier for the automatic assessment of peak integration quality of peaks from untargeted metabolomics analyses. The 11 peak quality metrics were adapted from those defined in the following references: Zhang, W., & Zhao, P.X. (2014) <doi:10.1186/1471-2105-15-S11-S5> Toghi Eshghi, S., Auger, P., & Mathews, W.R. (2018) <doi:10.1186/s12014-018-9209-x>.

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s4vectorslow-quality-integrationmachine-learningmetabolomics

3.40 score 5 stars 9 scripts 4 downloads

MS2Quant - Ionization efficiency prediction and quantification of unidentified chemicals

MS2Quant harvests pre-trained xgbTree algorithm-based ionization efficiency prediction model. Using strucutral information (SMILES) or predicted fingerprints calculated with SIRIUS+CSI_FingerID software, ionization efficiency can be predicted. If calibrants have been measured together with suspects subject to quantification, predicted ionization efficiencies can be converted into measurement-specific response factors and concentration of unknown chemcals can be estimated.

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openjdk

3.18 score 5 stars 6 scripts

Rmstoolkitlib - Wrapper Package for For MSToolkit

A simple wrapper package that exposes MSToolkit (https://github.com/mhoopmann/mstoolkit).

Last updated

2.48 score 1 stars

patRoonInst - Manages 'patRoon' Installations

Installs and updates patRoon and its dependencies.

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1.70 score 1 scripts

nontarget - Detecting Isotope, Adduct and Homologue Relations in LC-MS Data

Screening a HRMS data set for peaks related by (1) isotope patterns, (2) different adducts of the same molecule and/or (3) homologue series. The resulting isotopic pattern and adduct groups can then be combined to so-called components, with homologue series information attached. Also allows plotting and filtering HRMS data for mass defects, frequent m/z distances and components vs. non-components.

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cpp

2.78 score 4 stars 19 scripts

InterpretMSSpectrum - Interpreting High Resolution Mass Spectra

High resolution mass spectrometry yields often large data sets of spectra from compounds which are not present in available libraries. These spectra need to be annotated and interpreted.'InterpretMSSpectrum' provides a set of functions to perform such tasks for Electrospray-Ionization and Atmospheric-Pressure-Chemical-Ionization derived data in positive and negative ionization mode.

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2.68 score 2 stars 2 dependents 8 scripts 651 downloads

KPIC - Mass Spectrometry-Based Metabolomics Using Pure Ion Chromatograms

KPIC2 is an effective platform for LC-MS based metabolomics using pure ion chromatograms, which is developed for metabolomics studies. KPIC2 can detect pure ions accurately, align PICs across samples, group PICs to annotate isotope and adduct PICs, fill missing peaks and pattern recognition. High-resolution mass spectrometers like TOF and Orbitrap are more suitable.

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cpp

1.70 score 3 scripts

enviPick - Peak Picking for High Resolution Mass Spectrometry Data

Sequential partitioning, clustering and peak detection of centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw data plot.

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cpp

1.60 score 1 stars 3 scripts 10 downloads

nontargetData - Quantized simulation data of isotope pattern centroids

Data sets for isotope pattern grouping of LC-HRMS peaks with package nontarget. Based on a vast set of unique PubChem molecular formulas, quantized (a) m/z, (b) m/z differences, (c) intensity ratios and (d) marker centroids of simulated centroid pairs are listed for different instrument resolutions.

Last updated

1.00 score 1 stars 6 downloads