specmine: Metabolomics and Spectral Data Analysis and Mining

Provides methods for metabolomics and spectral data analysis, including data import, preprocessing, visualization, univariate and multivariate analysis, machine learning, feature selection, and pathway analysis. The package supports analytical workflows for different data types used in metabolomics and spectroscopy. Some optional functionality uses the suggested packages 'cyjShiny' and 'specmine.datasets'. The package 'specmine.datasets' is maintained separately at <https://github.com/PedroFontao/specmine.datasets>.

Version:	3.1.8
Depends:	R (≥ 4.0.0)
Imports:	baseline, caret, compare, ellipse, genefilter, GGally, ggplot2, grDevices, graphics, impute, imputeTS, MASS, methods, Metrics, narray, pcaPP, plotly, pls, RColorBrewer, readJDX, stats, utils
Suggests:	clusterCrit, curl, dbscan, fastICA, ggdendro, KEGGgraph, KEGGREST, knitr, MAIT, mclust, pins, qdap, qpdf, RCurl, cyjShiny, reticulate, rgl, Rtsne, rmarkdown, scatterplot3d, specmine.datasets, uwot, randomForest, xcms
Published:	2026-08-05
DOI:	10.32614/CRAN.package.specmine
Author:	Christopher Costa [aut], Marcelo Maraschin [aut], Miguel Rocha [aut], Sara Cardoso [aut], Telma Afonso [aut], Bruno Pereira [aut], Pedro Fontão [aut, cre], C. Beleites [cph], Jie Hao [cph]
Maintainer:	Pedro Fontão <pedrofontao812004 at gmail.com>
BugReports:	https://github.com/PedroFontao/specmine/issues
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL:	https://github.com/PedroFontao/specmine
NeedsCompilation:	no
SystemRequirements:	Python (>= 3.5.2), Python module 'nmrglue'
Materials:	NEWS
CRAN checks:	specmine results

Documentation:

Reference manual:	specmine.html , specmine.pdf
Vignettes:	User guide to analyze 2D-NMR metabolomics' experiments using *specmine* package (source, R code)

Downloads:

Package source:	specmine_3.1.8.tar.gz
Windows binaries:	r-devel: not available, r-release: not available, r-oldrel: not available
macOS binaries:	r-release (arm64): specmine_3.1.8.tgz, r-oldrel (arm64): specmine_3.1.8.tgz, r-release (x86_64): specmine_3.1.8.tgz, r-oldrel (x86_64): specmine_3.1.8.tgz
Old sources:	specmine archive

Linking:

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