Package: omicsGMF
Type: Package
Authors@R: c(
        person("Alexandre", "Segers", role=c("aut", "cre", "fnd"), email="alexandresegers@outlook.com"),
        person("Cristian", "Castiglione", role=c("ctb"), email="cristian.castiglione@unipd.it"),
        person("Christophe", "Vanderaa", role = c("ctb"), email="christophe.vanderaa@ugent.be"),
        person("Davide", "Risso", role=c("ctb", "fnd"), email="davide.risso@unipd.it"),
        person("Lieven", "Clement", role=c("ctb", "fnd"), email="lieven.clement@ugent.be")
	)
Version: 1.1.0
Date: 2025-01-14
Title: Dimensionality reduction of (single-cell) omics data in R using omicsGMF
Description: omicsGMF is a Bioconductor package that uses the sgdGMF-framework of the \code{sgdGMF} package for highly performant 
    and fast matrix factorization that can be used for dimensionality reduction, visualization and imputation of omics
    data. It considers data from the general exponential family as input, and therefore suits the use of both RNA-seq
    (Poisson or Negative Binomial data) and proteomics data (Gaussian data). It does not require prior transformation of
    counts to the log-scale, because it rather optimizes the deviances from the data family specified. Also, it allows to 
    correct for known sample-level and feature-level covariates, therefore enabling visualization and dimensionality reduction
    upon batch correction. Last but not least, it deals with missing values, and allows to impute these after matrix 
    factorization, useful for proteomics data. This Bioconductor package allows input of SummarizedExperiment, 
    SingleCellExperiment, and QFeature classes.
biocViews: SingleCell, RNASeq, Proteomics, QualityControl, Preprocessing, 
        Normalization, Visualization, DimensionReduction, Transcriptomics,
        GeneExpression, Sequencing, Software,
        DataRepresentation, MassSpectrometry
Depends:
    R (>= 4.5.0),
    sgdGMF,
    SingleCellExperiment,
    scuttle,
    scater
Imports: 
    stats,
    utils,
    Matrix,
    S4Vectors,
    SummarizedExperiment,
    DelayedArray,
    MatrixGenerics,
    BiocSingular,
    BiocParallel,
    beachmat,
    ggplot2,
    methods,
    QFeatures
Suggests: 
    knitr,
    dplyr,
    testthat,
    BiocGenerics,
    BiocStyle,
    graphics,
    grDevices
License: Artistic-2.0
URL: https://github.com/statOmics/omicsGMF
BugReports: https://github.com/statOmics/omicsGMF/issues
Config/testthat/edition: 3
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Funding: This work was supported by grants from Ghent University Special Research Fund [BOF20/GOA/023] (A.S., L.C.),
    Research Foundation Flanders [FWO G062219N] (A.S., L.C.) and as WOG [W005325N] (L.C.). This work was supported by EU 
    funding within the MUR PNRR ``National Center for HPC, big data and quantum computing'' (Project no. CN00000013 CN1). 
    D.R. was also supported by the National Cancer Institute of the National Institutes of Health (U24CA289073). The 
    views and opinions expressed are only those of the authors and do not necessarily reflect those of the European Union 
    or the European Commission. Neither the European Union nor the European Commission can be held responsible for them.
git_url: https://git.bioconductor.org/packages/omicsGMF
git_branch: devel
git_last_commit: 66f9d2d
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
