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: 1.3.0 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 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: cmake libglpk-dev make libicu-dev libuv1-dev libxml2-dev libssl-dev zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-04-28 13:05:52 UTC RemoteUrl: https://github.com/bioc/omicsGMF RemoteRef: HEAD RemoteSha: 6e1ebb5abe07c850be48e7e841868b7bafa89bb8 NeedsCompilation: no Packaged: 2026-07-03 22:58:11 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