Ron Wehrens

Ron Wehrens

10 packages on CRAN

2 packages on Bioconductor

BioMark

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Variable selection methods are provided for several classification methods: the lasso/elastic net, PCLDA, PLSDA, and several t-tests. Two approaches for selecting cutoffs can be used, one based on the stability of model coefficients under perturbation, and the other on higher criticism.

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Functions and scripts used in the book "Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences" by Ron Wehrens, Springer (2011). Data used in the package are available from github.

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The package provides data sets used in the book "Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences" by Ron Wehrens, Springer (2011).

alsace

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Alternating Least Squares (or Multivariate Curve Resolution) for analytical chemical data, in particular hyphenated data where the first direction is a retention time axis, and the second a spectral axis. Package builds on the basic als function from the ALS package and adds functionality for high-throughput analysis, including definition of time windows, clustering of profiles, retention time correction, etcetera.

kohonen

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Functions to train self-organising maps (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.

ptw

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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.

metaMS

bioconductor
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MS-based metabolomics data processing and compound annotation pipeline.

wccsom

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SOMs can be useful tools to group patterns containing several peaks. If peaks do not always occur at exactly the same position, classical distance measures cannot be used. This package provides SOM technology using the weighted crosscorrelation (WCC) distance.

EmbedSOM

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Provides a smooth mapping of multidimensional points into low-dimensional space defined by a self-organizing map. Designed to work with 'FlowSOM' and flow-cytometry use-cases. See Kratochvil et al. (2019) <doi:10.1101/496869>.

pls

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Multivariate regression methods Partial Least Squares Regression (PLSR), Principal Component Regression (PCR) and Canonical Powered Partial Least Squares (CPPLS).

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Fast single trait Genome Wide Association Studies (GWAS) following the method described in Kang et al. (2010), <doi:10.1038/ng.548>. One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris.

statgenSTA

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Phenotypic analysis of field trials using mixed models with and without spatial components. One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (<http://www.vsni.co.uk/software/asreml-r>).