omicsGMF
Dimensionality reduction of (single-cell) omics data in R using omicsGMF
Bioconductor version: 3.24 · Package version: 1.3.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("omicsGMF")Details
| Maintainer | Alexandre Segers <alexandresegers@outlook.com> |
| Author | Alexandre Segers [aut, cre, fnd], Cristian Castiglione [ctb], Christophe Vanderaa [ctb], Davide Risso [ctb, fnd], Lieven Clement [ctb, fnd] |
| License | Artistic-2.0 |
| URL | https://github.com/statOmics/omicsGMF |
| Bug Reports | https://github.com/statOmics/omicsGMF/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataRepresentation, DimensionReduction, GeneExpression, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
| Package Short Url | https://bioconductor.org/packages/omicsGMF/ |
Citation
From within R, enter citation("omicsGMF"):
Alexandre Segers. omicsGMF: Dimensionality reduction of (single-cell) omics data in R using omicsGMF. doi:10.18129/B9.bioc.omicsGMF, R package version 1.3.0, https://bioconductor.org/packages/omicsGMF.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- Proteomics vignette: dimensionality reduction and imputation with omicsGMF
- RNA-seq vignette: dimensionality reduction with omicsGMF
Download
Follow the installation instructions to use this package in your R session.
| Source package | omicsGMF_1.3.0.tar.gz |
| Windows binary (x86_64) | omicsGMF_1.3.0.zip |
| macOS binary (arm64) | omicsGMF_1.3.0.tgz |
| macOS binary (x86_64) | omicsGMF_1.3.0.tgz |
Dependencies
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