Showing 21 of total 21 results (show query)
martin3141
spant:MR Spectroscopy Analysis Tools
Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Maintained by Martin Wilson. Last updated 15 hours ago.
brainmrimrsmrshubspectroscopyfortran
25 stars 8.52 score 81 scripts
kisungyou
Rdimtools:Dimension Reduction and Estimation Methods
We provide linear and nonlinear dimension reduction techniques. Intrinsic dimension estimation methods for exploratory analysis are also provided. For more details on the package, see the paper by You and Shung (2022) <doi:10.1016/j.simpa.2022.100414>.
Maintained by Kisung You. Last updated 2 years ago.
dimension-estimationdimension-reductionmanifold-learningsubspace-learningopenblascppopenmp
52 stars 8.37 score 186 scripts 8 dependents
bioc
PepsNMR:Pre-process 1H-NMR FID signals
This package provides R functions for common pre-procssing steps that are applied on 1H-NMR data. It also provides a function to read the FID signals directly in the Bruker format.
Maintained by Manon Martin. Last updated 5 months ago.
softwarepreprocessingvisualizationmetabolomicsdataimport
10 stars 6.62 score 23 scripts 1 dependents
ethanbass
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 12 days ago.
bioinformaticscheminformaticschromatographygc-fidhplchplc-dadhplc-pdahplv-uvmetabolomicsopen-dataopen-sciencereproducibilityreproducible-research
18 stars 6.36 score 8 scripts 1 dependents
rwehrens
ptw:Parametric Time Warping
Parametric Time Warping aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation). Both warping of peak profiles and of peak lists are supported. A vignette for the latter is contained in the inst/doc directory of the source package - the vignette source can be found on the package github site.
Maintained by Ron Wehrens. Last updated 3 years ago.
8 stars 6.31 score 57 scripts 10 dependents
nspyrison
spinifex:Manual Tours, Manual Control of Dynamic Projections of Numeric Multivariate Data
Data visualization tours animates linear projection of multivariate data as its basis (ie. orientation) changes. The 'spinifex' packages generates paths for manual tours by manipulating the contribution of a single variable at a time Cook & Buja (1997) <doi:10.1080/10618600.1997.10474754>. Other types of tours, such as grand (random walk) and guided (optimizing some objective function) are available in the 'tourr' package Wickham et al. <doi:10.18637/jss.v040.i02>. 'spinifex' builds on 'tourr' and can render tours with 'gganimate' and 'plotly' graphics, and allows for exporting as an .html widget and as an .gif, respectively. This work is fully discussed in Spyrison & Cook (2020) <doi:10.32614/RJ-2020-027>.
Maintained by Nicholas Spyrison. Last updated 3 months ago.
dimensionreductiontoursvisualization
3 stars 6.28 score 105 scripts 1 dependents
inra
Rnmr1D:Perform the Complete Processing of a Set of Proton Nuclear Magnetic Resonance Spectra
Perform the complete processing of a set of proton nuclear magnetic resonance spectra from the free induction decay (raw data) and based on a processing sequence (macro-command file). An additional file specifies all the spectra to be considered by associating their sample code as well as the levels of experimental factors to which they belong. More detail can be found in Jacob et al. (2017) <doi:10.1007/s11306-017-1178-y>.
Maintained by Daniel Jacob. Last updated 3 days ago.
8 stars 5.98 scorebioc
ASICS:Automatic Statistical Identification in Complex Spectra
With a set of pure metabolite reference spectra, ASICS quantifies concentration of metabolites in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty. The method and its statistical properties are described in Tardivel et al. (2017) <doi:10.1007/s11306-017-1244-5>.
Maintained by Gaëlle Lefort. Last updated 5 months ago.
softwaredataimportcheminformaticsmetabolomics
5.18 score 30 scripts
annajenul
UBayFS:A User-Guided Bayesian Framework for Ensemble Feature Selection (UBayFS)
Implements the user-guided Bayesian framework for ensemble feature selection (UBayFS) : Jenul et al., (2022) <doi:10.1007/s10994-022-06221-9>.
Maintained by Anna Jenul. Last updated 2 years ago.
bayesian-statisticsensemble-modelsfeature-selectionuser-knowledge
5 stars 5.11 score 13 scripts
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
7 stars 4.77 score 17 scriptsnspyrison
cheem:Interactively Explore Local Explanations with the Radial Tour
Given a non-linear model, calculate the local explanation. We purpose view the data space, explanation space, and model residuals as ensemble graphic interactive on a shiny application. After an observation of interest is identified, the normalized variable importance of the local explanation is used as a 1D projection basis. The support of the local explanation is then explored by changing the basis with the use of the radial tour <doi:10.32614/RJ-2020-027>; <doi:10.1080/10618600.1997.10474754>.
Maintained by Nicholas Spyrison. Last updated 1 years ago.
2 stars 4.73 score 54 scripts
pcruniversum
MBmca:Nucleic Acid Melting Curve Analysis
Lightweight utilities for nucleic acid melting curve analysis are important in life sciences and diagnostics. This software can be used for the analysis and presentation of melting curve data from microbead-based assays (surface melting curve analysis) and reactions in solution (e.g., quantitative PCR (qPCR), real-time isothermal Amplification). Further information are described in detail in two publications in The R Journal [ <https://journal.r-project.org/archive/2013-2/roediger-bohm-schimke.pdf>; <https://journal.r-project.org/archive/2015-1/RJ-2015-1.pdf>].
Maintained by Stefan Roediger. Last updated 4 years ago.
4 stars 4.53 score 17 scriptskisungyou
T4cluster:Tools for Cluster Analysis
Cluster analysis is one of the most fundamental problems in data science. We provide a variety of algorithms from clustering to the learning on the space of partitions. See Hennig, Meila, and Rocci (2016, ISBN:9781466551886) for general exposition to cluster analysis.
Maintained by Kisung You. Last updated 4 years ago.
6 stars 4.26 score 9 scripts 2 dependentskisungyou
Riemann:Learning with Data on Riemannian Manifolds
We provide a variety of algorithms for manifold-valued data, including Fréchet summaries, hypothesis testing, clustering, visualization, and other learning tasks. See Bhattacharya and Bhattacharya (2012) <doi:10.1017/CBO9781139094764> for general exposition to statistics on manifolds.
Maintained by Kisung You. Last updated 2 years ago.
10 stars 3.70 score 8 scriptskisungyou
TDAkit:Toolkit for Topological Data Analysis
Topological data analysis studies structure and shape of the data using topological features. We provide a variety of algorithms to learn with persistent homology of the data based on functional summaries for clustering, hypothesis testing, visualization, and others. We refer to Wasserman (2018) <doi:10.1146/annurev-statistics-031017-100045> for a statistical perspective on the topic.
Maintained by Kisung You. Last updated 4 years ago.
2 stars 2.30 score 4 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
3 stars 2.18 score
cran
gcxgclab:GCxGC Preprocessing and Analysis
Provides complete detailed preprocessing of two-dimensional gas chromatogram (GCxGC) samples. Baseline correction, smoothing, peak detection, and peak alignment. Also provided are some analysis functions, such as finding extracted ion chromatograms, finding mass spectral data, targeted analysis, and nontargeted analysis with either the 'National Institute of Standards and Technology Mass Spectral Library' or with the mass data. There are also several visualization methods provided for each step of the preprocessing and analysis.
Maintained by Stephanie Gamble. Last updated 1 years ago.
2.00 score
manuelperis
RpeakChrom:Tools for Chromatographic Column Characterization and Modelling Chromatographic Peak
The quantitative measurement and detection of molecules in HPLC should be carried out by an accurate description of chromatographic peaks. In this package non-linear fitting using a modified Gaussian model with a parabolic variance (PVMG) has been implemented to obtain the retention time and height at the peak maximum. This package also includes the traditional Van Deemter approach and two alternatives approaches to characterize chromatographic column.
Maintained by Manuel David Peris Diaz. Last updated 8 years ago.
1.00 score 4 scripts
guangbaog
FPCdpca:The FPCdpca Criterion on Distributed Principal Component Analysis
We consider optimal subset selection in the setting that one needs to use only one data subset to represent the whole data set with minimum information loss, and devise a novel intersection-based criterion on selecting optimal subset, called as the FPC criterion, to handle with the optimal sub-estimator in distributed principal component analysis; That is, the FPCdpca. The philosophy of the package is described in Guo G. (2020) <doi:10.1007/s00180-020-00974-4>.
Maintained by Guangbao Guo. Last updated 10 months ago.
1.00 score
caetanods
do3PCA:Probabilistic Phylogenetic Principal Component Analysis
Estimates probabilistic phylogenetic Principal Component Analysis (PCA) and non-phylogenetic probabilistic PCA. Provides methods to implement alternative models of trait evolution including Brownian motion (BM), Ornstein-Uhlenbeck (OU), Early Burst (EB), and Pagel's lambda. Also provides flexible biplot functions.
Maintained by Daniel Caetano. Last updated 6 months ago.
1.00 score