Package: ropls
Type: Package
Title: PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and
        feature selection of omics data
Version: 1.42.0
Date: 2024-09-13
Authors@R: 
    person("Etienne A.", "Thevenot", email = "etienne.thevenot@cea.fr", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1019-4577"))
biocViews: Regression, Classification, PrincipalComponent,
        Transcriptomics, Proteomics, Metabolomics, Lipidomics,
        MassSpectrometry, ImmunoOncology
Description: Latent variable modeling with Principal Component Analysis (PCA) and Partial Least Squares (PLS) are
    powerful methods for visualization, regression, classification, and feature selection of omics data where the
    number of variables exceeds the number of samples and with multicollinearity among variables. Orthogonal Partial
    Least Squares (OPLS) enables to separately model the variation correlated (predictive) to the factor of interest
    and the uncorrelated (orthogonal) variation. While performing similarly to PLS, OPLS facilitates interpretation.
    Successful applications of these chemometrics techniques include spectroscopic data such as Raman spectroscopy,
    nuclear magnetic resonance (NMR), mass spectrometry (MS) in metabolomics and proteomics, but also transcriptomics
    data. In addition to scores, loadings and weights plots, the package provides metrics and graphics to determine 
    the optimal number of components (e.g. with the R2 and Q2 coefficients), check the validity of the model by 
    permutation testing, detect outliers, and perform feature selection (e.g. with Variable Importance in Projection 
    or regression coefficients). The package can be accessed via a user interface on the Workflow4Metabolomics.org 
    online resource for computational metabolomics (built upon the Galaxy environment).
Depends: R (>= 3.5.0)
Imports: Biobase, ggplot2, graphics, grDevices, methods, plotly, stats,
        MultiAssayExperiment, MultiDataSet, SummarizedExperiment, utils
Suggests: BiocGenerics, BiocStyle, knitr, multtest, omicade4, phenomis,
        rmarkdown, testthat
VignetteBuilder: knitr
License: CeCILL
Encoding: UTF-8
LazyLoad: yes
URL: https://doi.org/10.1021/acs.jproteome.5b00354
NeedsCompilation: no
RoxygenNote: 7.2.3
Packaged: 2025-10-30 05:12:32 UTC; biocbuild
git_url: https://git.bioconductor.org/packages/ropls
git_branch: RELEASE_3_22
git_last_commit: 7e60063
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
Author: Etienne A. Thevenot [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1019-4577>)
Maintainer: Etienne A. Thevenot <etienne.thevenot@cea.fr>
Built: R 4.5.1; ; 2025-10-30 12:35:43 UTC; unix
