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metaboData - Example Metabolomics Data Sets

Data sets from a variety of biological sample matrices, analysed using a number of mass spectrometry based metabolomic analytical techniques. The example data sets are stored remotely using GitHub releases <https://github.com/aberHRML/metaboData/releases> which can be accessed from R using the package. The package also includes the 'abr1' FIE-MS data set from the 'FIEmspro' package <https://github.com/aberHRML/FIEmspro> <doi:10.1038/nprot.2007.511>.

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datadatasetsfie-hrmsfie-msmass-spectrometrymetabolomics

5.00 score 2 stars 101 scripts 433 downloads

pdi - Phenotypic Index Measures for Oak Decline Severity

Oak declines are complex disease syndromes and consist of many visual indicators that include aspects of tree size, crown condition and trunk condition. This can cause difficulty in the manual classification of symptomatic and non-symptomatic trees from what is in reality a broad spectrum of oak tree health condition. Two phenotypic oak decline indexes have been developed to quantitatively describe and differentiate oak decline syndromes in Quercus robur. This package provides a toolkit to generate these decline indexes from phenotypic descriptors using the machine learning algorithm random forest. The methodology for generating these indexes is outlined in Finch et al. (2021) <doi:10.1016/j.foreco.2021.118948>.

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declineindexoakphenotyping

3.70 score 417 downloads

binneR - Spectral Processing for High Resolution Flow Infusion Mass Spectrometry

A spectral binning approach for flow infusion electrospray high resolution mass spectrometry (FIE-HRMS) metabolome fingerprinting data. The methodology for this approach is outlined in Finch et al. (2022) <doi:10.1007/s11306-022-01923-6>.

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massspectrometrymetabolomicsfie-hrmsfingerprintinghigh-resolution-mass-spectrometrymass-spectrometryspectral-binning

3.45 score 4 stars 14 scripts 48 downloads

metabolyseR - Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data

A tool kit for pre-treatment, modelling, feature selection and correlation analyses of metabolomics data.

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metabolomics

3.30 score 7 scripts