Showing 25 of total 25 results (show query)
bioc
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
17.3 match 15 stars 7.50 score 15 scripts
idslme
IDSL.FSA:Fragmentation Spectra Analysis (FSA)
The 'IDSL.FSA' package was designed to annotate standard .msp (mass spectra format) and .mgf (Mascot generic format) files using mass spectral entropy similarity, dot product (cosine) similarity, and normalized Euclidean mass error (NEME) followed by intelligent pre-filtering steps for rapid spectra searches. 'IDSL.FSA' also provides a number of modules to convert and manipulate .msp and .mgf files. The 'IDSL.FSA' workflow was integrated in the 'IDSL.CSA' and 'IDSL.NPA' packages introduced in <doi:10.1021/acs.analchem.3c00376>.
Maintained by Dinesh Barupal. Last updated 7 months ago.
fragmentation-spectramass-spectrometrymassbankmgfmgf-parsermspmsp-parserspectral-entropy
34.8 match 1 stars 3.48 score 2 dependentsbioc
MsBackendMsp:Mass Spectrometry Data Backend for NIST msp Files
Mass spectrometry (MS) data backend supporting import and handling of MS/MS spectra from NIST MSP Format (msp) files. Import of data from files with different MSP *flavours* is supported. Objects from this package add support for MSP files to Bioconductor's Spectra package. This package is thus not supposed to be used without the Spectra package that provides a complete infrastructure for MS data handling.
Maintained by Johannes Rainer. Last updated 2 months ago.
infrastructureproteomicsmassspectrometrymetabolomicsdataimportmass-spectrometry
10.2 match 5 stars 7.22 score 37 scripts 3 dependents
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.
8.3 match 12 stars 6.78 score 20 scripts
wenjie2wang
splines2:Regression Spline Functions and Classes
Constructs basis functions of B-splines, M-splines, I-splines, convex splines (C-splines), periodic splines, natural cubic splines, generalized Bernstein polynomials, their derivatives, and integrals (except C-splines) by closed-form recursive formulas. It also contains a C++ head-only library integrated with Rcpp. See Wang and Yan (2021) <doi:10.6339/21-JDS1020> for details.
Maintained by Wenjie Wang. Last updated 12 days ago.
derivativeintegralrcppsplinesopenblascpp
3.3 match 43 stars 11.46 score 394 scripts 34 dependents
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
5.1 match 17 stars 6.49 score 30 scripts 1 dependentsbioc
mspms:Tools for the analysis of MSP-MS data
This package provides functions for the analysis of data generated by the multiplex substrate profiling by mass spectrometry for proteases (MSP-MS) method. Data exported from upstream proteomics software is accepted as input and subsequently processed for analysis. Tools for statistical analysis, visualization, and interpretation of the data are provided.
Maintained by Charlie Bayne. Last updated 3 months ago.
proteomicsmassspectrometrypreprocessingproteaseproteomics-data-analysis
6.6 match 4.95 score 4 scriptsbioc
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
4.0 match 4 stars 7.42 score 3 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.
5.7 match 5 stars 4.70 score 20 scriptsidslme
IDSL.CSA:Composite Spectra Analysis (CSA) for High-Resolution Mass Spectrometry Analyses
A fragmentation spectra detection pipeline for high-throughput LC/HRMS data processing using peaklists generated by the 'IDSL.IPA' workflow <doi:10.1021/acs.jproteome.2c00120>. The 'IDSL.CSA' package can deconvolute fragmentation spectra from Composite Spectra Analysis (CSA), Data Dependent Acquisition (DDA) analysis, and various Data-Independent Acquisition (DIA) methods such as MS^E, All-Ion Fragmentation (AIF) and SWATH-MS analysis. The 'IDSL.CSA' package was introduced in <doi:10.1021/acs.analchem.3c00376>.
Maintained by Dinesh Barupal. Last updated 2 years ago.
composite-spectra-analysiscsadata-dependent-acquisitiondata-independent-acquisitionddadiamass-spectrometrymetabolomicsmetabolomics-pipelinesmall-moleculespectral-entropy
7.8 match 5 stars 3.40 scoreyufree
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
3.4 match 10 stars 6.68 score 40 scriptsbioc
msPurity:Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
msPurity R package was developed to: 1) Assess the spectral quality of fragmentation spectra by evaluating the "precursor ion purity". 2) Process fragmentation spectra. 3) Perform spectral matching. What is precursor ion purity? -What we call "Precursor ion purity" is a measure of the contribution of a selected precursor peak in an isolation window used for fragmentation. The simple calculation involves dividing the intensity of the selected precursor peak by the total intensity of the isolation window. When assessing MS/MS spectra this calculation is done before and after the MS/MS scan of interest and the purity is interpolated at the recorded time of the MS/MS acquisition. Additionally, isotopic peaks can be removed, low abundance peaks are removed that are thought to have limited contribution to the resulting MS/MS spectra and the isolation efficiency of the mass spectrometer can be used to normalise the intensities used for the calculation.
Maintained by Thomas N. Lawson. Last updated 5 months ago.
massspectrometrymetabolomicssoftwarebioconductor-packagedimsfragmentationlc-mslc-msmsmass-spectrometryprecursor-ion-purity
2.9 match 15 stars 7.03 score 44 scripts
cran
OrgMassSpecR:Organic Mass Spectrometry
Organic/biological mass spectrometry data analysis.
Maintained by Nathan Dodder. Last updated 8 years ago.
5.3 match 3.68 score 2 dependents
andreysamokhin
mssearchr:Library Search Against Electron Ionization Mass Spectral Databases
Perform library searches against electron ionization mass spectral databases using either the API provided by 'MS Search' software (<https://chemdata.nist.gov/dokuwiki/doku.php?id=chemdata:nistlibs>) or custom implementations of the Identity and Similarity algorithms.
Maintained by Andrey Samokhin. Last updated 3 months ago.
3.4 match 2 stars 3.48 score 1 scriptsbioc
RMassBank:Workflow to process tandem MS files and build MassBank records
Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.
Maintained by RMassBank at Eawag. Last updated 5 months ago.
immunooncologybioinformaticsmassspectrometrymetabolomicssoftwareopenjdk
1.9 match 6.19 score 26 scriptsidslme
IDSL.NPA:Nominal Peak Analysis (NPA)
A pipeline to process nominal mass spectrometry data to create .msp files for untargeted analyses.
Maintained by Dinesh Barupal. Last updated 2 years ago.
gcmsmass-spectrometrymetabolomicsspectral-entropy
4.2 match 1 stars 2.70 score
rickhelmus
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.
Maintained by Rick Helmus. Last updated 10 days ago.
mass-spectrometrynon-targetcppopenjdk
1.8 match 65 stars 6.22 score 43 scripts
gabrielodom
mvMonitoring:Multi-State Adaptive Dynamic Principal Component Analysis for Multivariate Process Monitoring
Use multi-state splitting to apply Adaptive-Dynamic PCA (ADPCA) to data generated from a continuous-time multivariate industrial or natural process. Employ PCA-based dimension reduction to extract linear combinations of relevant features, reducing computational burdens. For a description of ADPCA, see <doi:10.1007/s00477-016-1246-2>, the 2016 paper from Kazor et al. The multi-state application of ADPCA is from a manuscript under current revision entitled "Multi-State Multivariate Statistical Process Control" by Odom, Newhart, Cath, and Hering, and is expected to appear in Q1 of 2018.
Maintained by Gabriel Odom. Last updated 1 years ago.
1.5 match 4 stars 5.24 score 29 scriptsbioc
MetCirc:Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data
MetCirc comprises a workflow to interactively explore high-resolution MS/MS metabolomics data. MetCirc uses the Spectra object infrastructure defined in the package Spectra that stores MS/MS spectra. MetCirc offers functionality to calculate similarity between precursors based on the normalised dot product, neutral losses or user-defined functions and visualise similarities in a circular layout. Within the interactive framework the user can annotate MS/MS features based on their similarity to (known) related MS/MS features.
Maintained by Thomas Naake. Last updated 5 months ago.
shinyappsmetabolomicsmassspectrometryvisualization
1.7 match 3.48 score 3 scriptscran
fat2Lpoly:Two-Locus Family-Based Association Test with Polytomous Outcome
Performs family-based association tests with a polytomous outcome under 2-locus and 1-locus models defined by some design matrix.
Maintained by Alexandre BUREAU. Last updated 3 years ago.
1.6 match 1.00 score
s6sebusc
dualtrees:Decimated and Undecimated 2D Complex Dual-Tree Wavelet Transform
An implementation of the decimated two-dimensional complex dual-tree wavelet transform as described in Kingsbury (1999) <doi:10.1098/rsta.1999.0447> and Selesnick et al. (2005) <doi:10.1109/MSP.2005.1550194>. Also includes the undecimated version and spectral bias correction described in Nelson et al. (2018) <doi:10.1007/s11222-017-9784-0>. The code is partly based on the 'dtcwt' Python library.
Maintained by Sebastian Buschow. Last updated 1 years ago.
0.5 match 3.18 score 1 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
0.5 match 3 stars 2.78 score
