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 (>= 4.4.0), 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
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.
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libglpk-dev make
        libharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev
        libwebp-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:39:15 UTC
RemoteUrl: https://github.com/bioc/omicsGMF
RemoteRef: HEAD
RemoteSha: 66f9d2d59adb899f0d19401e95004180a82c909b
NeedsCompilation: no
Packaged: 2026-01-09 21:35:40 UTC; root
Author: Alexandre Segers [aut, cre, fnd],
  Cristian Castiglione [ctb],
  Christophe Vanderaa [ctb],
  Davide Risso [ctb, fnd],
  Lieven Clement [ctb, fnd]
Maintainer: Alexandre Segers <alexandresegers@outlook.com>
Built: R 4.6.0; ; 2026-01-09 21:38:51 UTC; windows
