Showing 13 of total 13 results (show query)
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
67.2 match 196 stars 14.31 score 984 scripts 11 dependentsbioc
metaMS:MS-based metabolomics annotation pipeline
MS-based metabolomics data processing and compound annotation pipeline.
Maintained by Yann Guitton. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomics
82.1 match 15 stars 7.50 score 15 scripts
yufree
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
65.9 match 17 stars 6.49 score 30 scripts 1 dependentsbioc
TargetSearch:A package for the analysis of GC-MS metabolite profiling data
This packages provides a flexible, fast and accurate method for targeted pre-processing of GC-MS data. The user provides a (often very large) set of GC chromatograms and a metabolite library of targets. The package will automatically search those targets in the chromatograms resulting in a data matrix that can be used for further data analysis.
Maintained by Alvaro Cuadros-Inostroza. Last updated 4 months ago.
massspectrometrypreprocessingdecisiontreeimmunooncologybiocbioconductorgc-msmass-spectrometry
53.9 match 4 stars 7.42 score 3 scripts
idslme
IDSL.MXP:Parser for mzML, mzXML, and netCDF Files (Mass Spectrometry Data)
A tiny parser to extract mass spectra data and metadata table of mass spectrometry acquisition properties from mzML, mzXML and netCDF files introduced in <doi:10.1021/acs.jproteome.2c00120>.
Maintained by Dinesh Barupal. Last updated 2 years ago.
exposomegc-ms-datalc-ms-datalipidomicsmass-spectrometrymetabolomicsmzmlmzxmlnetcdf
20.0 match 5 stars 4.57 score 1 scripts 5 dependents
ethanbass
mzinspectr:Read and Analyze Mass Spectrometry Alignment Files
A few functions for analyzing MS-DIAL alignments in R. Includes functions for feature normalization, subtraction of blanks, and mass library (msp) search.
Maintained by Ethan Bass. Last updated 5 months ago.
cheminformaticsgc-mslc-msmetabolomics
29.9 match 3 stars 2.78 scorebioc
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
17.0 match 4.30 score 2 scriptsethanbass
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
12.0 match 2 stars 4.26 score 2 scripts 2 dependents
xdomingoal
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.
29.0 match 1.62 score 14 scripts 1 dependentsbioc
SIMAT:GC-SIM-MS data processing and alaysis tool
This package provides a pipeline for analysis of GC-MS data acquired in selected ion monitoring (SIM) mode. The tool also provides a guidance in choosing appropriate fragments for the targets of interest by using an optimization algorithm. This is done by considering overlapping peaks from a provided library by the user.
Maintained by M. R. Nezami Ranjbar. Last updated 5 months ago.
immunooncologysoftwaremetabolomicsmassspectrometry
10.2 match 4.26 score 1 scriptsxdomingoal
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.
6.5 match 5 stars 4.70 score 20 scripts
janlisec
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.
9.2 match 3.18 score 5 scripts 1 dependents
bryanhanson
readJDX:Import Data in the JCAMP-DX Format
Import data written in the JCAMP-DX format. This is an instrument-independent format used in the field of spectroscopy. Examples include IR, NMR, and Raman spectroscopy. See the vignette for background and supported formats. The official JCAMP-DX site is <http://www.jcamp-dx.org/>.
Maintained by Bryan A. Hanson. Last updated 1 years ago.
3.5 match 8 stars 6.48 score 7 scripts 5 dependents