Showing 29 of total 29 results (show query)
mottensmann
GCalignR:Simple Peak Alignment for Gas-Chromatography Data
Aligns peak based on peak retention times and matches homologous peaks across samples. The underlying alignment procedure comprises three sequential steps. (1) Full alignment of samples by linear transformation of retention times to maximise similarity among homologous peaks (2) Partial alignment of peaks within a user-defined retention time window to cluster homologous peaks (3) Merging rows that are likely representing homologous substances (i.e. no sample shows peaks in both rows and the rows have similar retention time means). The algorithm is described in detail in Ottensmann et al., 2018 <doi:10.1371/journal.pone.0198311>.
Maintained by Meinolf Ottensmann. Last updated 6 months ago.
15.0 match 5 stars 6.39 score 41 scripts
ethanbass
chromConverter:Chromatographic File Converter
Reads chromatograms from binary formats into R objects. Currently supports conversion of 'Agilent ChemStation', 'Agilent MassHunter', 'Shimadzu LabSolutions', 'ThermoRaw', and 'Varian Workstation' files as well as various text-based formats. In addition to its internal parsers, chromConverter contains bindings to parsers in external libraries, such as 'Aston' <https://github.com/bovee/aston>, 'Entab' <https://github.com/bovee/entab>, 'rainbow' <https://rainbow-api.readthedocs.io/>, and 'ThermoRawFileParser' <https://github.com/compomics/ThermoRawFileParser>.
Maintained by Ethan Bass. Last updated 10 days ago.
cheminformaticschromatographyfair-datagc-fidhplchplc-dadhplc-uvmetabolomicsmetabolomics-dataopen-dataopen-science
11.5 match 33 stars 6.35 score 16 scripts 2 dependents
bioc
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.
Maintained by Steffen Neumann. Last updated 2 days ago.
immunooncologymassspectrometrymetabolomicsbioconductorfeature-detectionmass-spectrometrypeak-detectioncpp
5.0 match 196 stars 14.31 score 984 scripts 11 dependentsethanbass
chromatographR:Chromatographic Data Analysis Toolset
Tools for high-throughput analysis of HPLC-DAD/UV chromatograms (or similar data). Includes functions for preprocessing, alignment, peak-finding and fitting, peak-table construction, data-visualization, etc. Preprocessing and peak-table construction follow the rough formula laid out in 'alsace' (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C., 2015. <doi:10.1093/bioinformatics/btv299>. Alignment of chromatograms is available using parametric time warping (as implemented in the 'ptw' package) (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C. 2015. <doi:10.1093/bioinformatics/btv299>) or variable penalty dynamic time warping (as implemented in 'VPdtw') (Clifford, D., & Stone, G. 2012. <doi:10.18637/jss.v047.i08>). Peak-finding uses the algorithm by Tom O'Haver <https://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm>. Peaks are then fitted to a gaussian or exponential-gaussian hybrid peak shape using non-linear least squares (Lan, K. & Jorgenson, J. W. 2001. <doi:10.1016/S0021-9673(01)00594-5>). See the vignette for more details and suggested workflow.
Maintained by Ethan Bass. Last updated 9 days ago.
bioinformaticscheminformaticschromatographygc-fidhplchplc-dadhplc-pdahplv-uvmetabolomicsopen-dataopen-sciencereproducibilityreproducible-research
10.0 match 18 stars 6.33 score 8 scripts 1 dependentsethanbass
VPdtw:Variable Penalty Dynamic Time Warping
Variable Penalty Dynamic Time Warping (VPdtw) for aligning chromatographic signals. With an appropriate penalty this method performs good alignment of chromatographic data without deforming the peaks (Clifford, D., Stone, G., Montoliu, I., Rezzi S., Martin F., Guy P., Bruce S., and Kochhar S.(2009) <doi:10.1021/ac802041e>; Clifford, D. and Stone, G. (2012) <doi:10.18637/jss.v047.i08>).
Maintained by Ethan Bass. Last updated 7 months ago.
chemoinformaticschemometricschromatographytime-seriestime-warpingcpp
10.0 match 2 stars 4.26 score 2 scripts 2 dependentsbioc
yamss:Tools for high-throughput metabolomics
Tools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis. At the core of these methods is a peak detection phase that pools information across all samples simultaneously. This is in contrast to other methods that detect peaks in a sample-by-sample basis.
Maintained by Leslie Myint. Last updated 5 months ago.
massspectrometrymetabolomicspeakdetectionsoftware
5.6 match 3 stars 5.08 score 9 scriptsethanbass
ShinyChromViewer:Shiny Gadget for Interactive Viewing and Exploration of Chromatograms
Shiny Gadget for interactive viewing and exploration of chromatograms.
Maintained by Ethan Bass. Last updated 2 years ago.
chromatographyhplchplc-dadhplc-uvopen-dataopen-scienceshinyshiny-apps
10.0 match 3 stars 2.18 score
bradyajohnston
chromr:Read and Plot FPLC Chromatograms
For reading files from BioRad QuadTec machines and making plots of the charomatograms.
Maintained by Brady Johnston. Last updated 2 years ago.
10.0 match 1.70 score
danielquiroz97
RGCxGC:Preprocessing and Multivariate Analysis of Bidimensional Gas Chromatography Data
Toolbox for chemometrics analysis of bidimensional gas chromatography data. This package import data for common scientific data format (NetCDF) and fold it to 2D chromatogram. Then, it can perform preprocessing and multivariate analysis. In the preprocessing algorithms, baseline correction, smoothing, and peak alignment are available. While in multivariate analysis, multiway principal component analysis is incorporated.
Maintained by Cristian Quiroz-Moreno. Last updated 2 years ago.
chemphyschemometricsgcxgcmultiway-algorithmspreprocessing
3.4 match 7 stars 4.77 score 17 scripts
spang-lab
FastRet:Retention Time Prediction in Liquid Chromatography
A framework for predicting retention times in liquid chromatography. Users can train custom models for specific chromatography columns, predict retention times using existing models, or adjust existing models to account for altered experimental conditions. The provided functionalities can be accessed either via the R console or via a graphical user interface. Related work: Bonini et al. (2020) <doi:10.1021/acs.analchem.9b05765>.
Maintained by Tobias Schmidt. Last updated 1 months ago.
retentiontimechromotographylc-msdata-sciencelcmsopenjdk
3.8 match 3.48 score 4 scripts
adafede
cascade:Contextualizing untargeted Annotation with Semi-quantitative Charged Aerosol Detection for pertinent characterization of natural Extracts
This package provides the infrastructure to perform Automated Composition Assessment of Natural Extracts.
Maintained by Adriano Rutz. Last updated 11 days ago.
metabolite annotationcharged aerosol detectorsemi-quantitativenatural productscomputational metabolomicsspecialized metabolome
2.3 match 2 stars 5.74 score 40 scripts 1 dependents
idslme
IDSL.IPA:Intrinsic Peak Analysis (IPA) for HRMS Data
A multi-layered untargeted pipeline for high-throughput LC/HRMS data processing to extract signals of organic small molecules. The package performs ion pairing, peak detection, peak table alignment, retention time correction, aligned peak table gap filling, peak annotation and visualization of extracted ion chromatograms (EICs) and total ion chromatograms (TICs). The 'IDSL.IPA' package was introduced in <doi:10.1021/acs.jproteome.2c00120> .
Maintained by Dinesh Barupal. Last updated 2 years ago.
exposomefeature-detectionlipidomicsmass-spectrometrymetabolomicspeak-detectionpeak-pickingsmall-moleculeuntargeted-metabolomics
2.3 match 13 stars 4.89 score 1 scripts 4 dependentsbioc
MsQuality:MsQuality - Quality metric calculation from Spectra and MsExperiment objects
The MsQuality provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteom Organization-Proteomics Standards Initiative (HUPO-PSI). These metrics quantify the quality of spectral raw files using a controlled vocabulary. The package is especially addressed towards users that acquire mass spectrometry data on a large scale (e.g. data sets from clinical settings consisting of several thousands of samples). The MsQuality package allows to calculate low-level quality metrics that require minimum information on mass spectrometry data: retention time, m/z values, and associated intensities. MsQuality relies on the Spectra package, or alternatively the MsExperiment package, and its infrastructure to store spectral data.
Maintained by Thomas Naake. Last updated 2 months ago.
metabolomicsproteomicsmassspectrometryqualitycontrolmass-spectrometryqc
1.9 match 7 stars 5.45 score 2 scripts
janlisec
CorMID:Correct Mass Isotopologue Distribution Vectors
In metabolic flux experiments tracer molecules (often glucose containing labelled carbon) are incorporated in compounds measured using mass spectrometry. The mass isotopologue distributions of these compounds needs to be corrected for natural abundance of labelled carbon and other effects, which are specific on the compound and ionization technique applied. This package provides functions to correct such effects in gas chromatography atmospheric pressure chemical ionization mass spectrometry analyses.
Maintained by Jan Lisec. Last updated 2 months ago.
1.8 match 4.88 score 3 scripts 1 dependents
jaehyunjoo
LCMSQA:Liquid Chromatography/Mass Spectrometry (LC/MS) Quality Assessment
The goal of 'LCMSQA' is to make it easy to check the quality of liquid chromatograph/mass spectrometry (LC/MS) experiments using a 'shiny' application. This package provides interactive data visualizations for quality control (QC) samples, including total ion current chromatogram (TIC), base peak chromatogram (BPC), mass spectrum, extracted ion chromatogram (XIC), and feature detection results from internal standards or known metabolites.
Maintained by Jaehyun Joo. Last updated 1 years ago.
2.8 match 2.70 score 2 scripts
ivanp84
qtlc:Densitometric Analysis of Thin-Layer Chromatography Plates
Densitometric evaluation of the photo-archived quantitative thin-layer chromatography (TLC) plates.
Maintained by Ivan D. Pavicevic. Last updated 9 years ago.
3.5 match 1 stars 1.34 score 22 scriptsbioc
IPO:Automated Optimization of XCMS Data Processing parameters
The outcome of XCMS data processing strongly depends on the parameter settings. IPO (`Isotopologue Parameter Optimization`) is a parameter optimization tool that is applicable for different kinds of samples and liquid chromatography coupled to high resolution mass spectrometry devices, fast and free of labeling steps. IPO uses natural, stable 13C isotopes to calculate a peak picking score. Retention time correction is optimized by minimizing the relative retention time differences within features and grouping parameters are optimized by maximizing the number of features showing exactly one peak from each injection of a pooled sample. The different parameter settings are achieved by design of experiment. The resulting scores are evaluated using response surface models.
Maintained by Thomas Lieb. Last updated 5 months ago.
immunooncologymetabolomicsmassspectrometry
0.5 match 34 stars 8.14 score 41 scripts
cbroeckl
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 <DOI: 10.1021/ac501530d> data.
Maintained by Helge Hecht. Last updated 7 months ago.
0.5 match 12 stars 6.78 score 20 scriptsbioc
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.
Maintained by Oriol Senan Campos. Last updated 5 months ago.
metabolomicsmassspectrometrynetworknetworkinferencecpp
0.5 match 12 stars 6.91 score 25 scriptsbioc
rawDiag:Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful
Optimizing methods for liquid chromatography coupled to mass spectrometry (LC-MS) poses a nontrivial challenge. The rawDiag package facilitates rational method optimization by generating MS operator-tailored diagnostic plots of scan-level metadata. The package is designed for use on the R shell or as a Shiny application on the Orbitrap instrument PC.
Maintained by Christian Panse. Last updated 4 months ago.
massspectrometryproteomicsmetabolomicsinfrastructuresoftwareshinyappsfastmass-spectrometrymultiplatformorbitrapvisualization
0.5 match 36 stars 6.71 score 18 scripts
yufree
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.
Maintained by Miao YU. Last updated 2 months ago.
mass-spectrometrymetabolomicsnon-target
0.5 match 10 stars 6.68 score 40 scriptsyufree
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.
Maintained by Miao YU. Last updated 2 months ago.
environmentmass-spectrometrymetabolomics
0.5 match 17 stars 6.49 score 30 scripts 1 dependentsbioc
flagme:Analysis of Metabolomics GC/MS Data
Fragment-level analysis of gas chromatography-massspectrometry metabolomics data.
Maintained by Mark Robinson. Last updated 5 months ago.
differentialexpressionmassspectrometry
0.6 match 4.30 score 2 scripts
xdomingoal
erah:Automated Spectral Deconvolution, Alignment, and Metabolite Identification in GC/MS-Based Untargeted Metabolomics
Automated compound deconvolution, alignment across samples, and identification of metabolites by spectral library matching in Gas Chromatography - Mass spectrometry (GC-MS) untargeted metabolomics. Outputs a table with compound names, matching scores and the integrated area of the compound for each sample. Package implementation is described in Domingo-Almenara et al. (2016) <doi:10.1021/acs.analchem.6b02927>.
Maintained by Xavier Domingo-Almenara. Last updated 1 years ago.
0.5 match 5 stars 4.70 score 20 scriptsbioc
cosmiq:cosmiq - COmbining Single Masses Into Quantities
cosmiq is a tool for the preprocessing of liquid- or gas - chromatography mass spectrometry (LCMS/GCMS) data with a focus on metabolomics or lipidomics applications. To improve the detection of low abundant signals, cosmiq generates master maps of the mZ/RT space from all acquired runs before a peak detection algorithm is applied. The result is a more robust identification and quantification of low-intensity MS signals compared to conventional approaches where peak picking is performed in each LCMS/GCMS file separately. The cosmiq package builds on the xcmsSet object structure and can be therefore integrated well with the package xcms as an alternative preprocessing step.
Maintained by David Fischer. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomics
0.5 match 4.48 score 2 scriptsidslme
IDSL.UFA:United Formula Annotation (UFA) for HRMS Data Processing
A pipeline to annotate chromatography peaks from the 'IDSL.IPA' workflow <doi:10.1021/acs.jproteome.2c00120> with molecular formulas of a prioritized chemical space using an isotopic profile matching approach. The 'IDSL.UFA' workflow only requires mass spectrometry level 1 (MS1) data for formula annotation. The 'IDSL.UFA' methods was described in <doi:10.1021/acs.analchem.2c00563> .
Maintained by Dinesh Barupal. Last updated 2 years ago.
exposomeisotopic-distribution-calculationslipidomicsmass-spectrometrymetabolomicsmolecular-formulae-assignmentsmall-molecule
0.5 match 8 stars 4.08 score 1 scripts 1 dependentsjanlisec
CorrectOverloadedPeaks:Correct Overloaded Peaks from GC-APCI-MS Data
Analyzes and modifies metabolomics raw data (generated using Gas Chromatography-Atmospheric Pressure Chemical Ionization-Mass Spectrometry) to correct overloaded signals, i.e. ion intensities exceeding detector saturation leading to a cut-off peak. Data in 'xcmsRaw' format are accepted as input and 'mzXML' files can be processed alternatively. Overloaded signals are detected automatically and modified using an Gaussian or an Isotopic-Ratio approach. Quality control plots are generated and corrected data are stored within the original 'xcmsRaw' or 'mzXML' respectively to allow further processing.
Maintained by Jan Lisec. Last updated 18 days ago.
0.5 match 3.18 score 5 scripts 1 dependentsxdomingoal
osd:Orthogonal Signal Deconvolution for Spectra Deconvolution in GC-MS and GCxGC-MS Data
Compound deconvolution for chromatographic data, including gas chromatography - mass spectrometry (GC-MS) and comprehensive gas chromatography - mass spectrometry (GCxGC-MS). The package includes functions to perform independent component analysis - orthogonal signal deconvolution (ICA-OSD), independent component regression (ICR), multivariate curve resolution (MCR-ALS) and orthogonal signal deconvolution (OSD) alone.
Maintained by Xavier Domingo-Almenara. Last updated 9 years ago.
0.8 match 1.62 score 14 scripts 1 dependents
