omicsGMF
This is the released version of omicsGMF; for the devel version, see omicsGMF.
Dimensionality reduction of (single-cell) omics data in R using omicsGMF
Bioconductor version: Release (3.23)
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.
Author: Alexandre Segers [aut, cre, fnd], Cristian Castiglione [ctb], Christophe Vanderaa [ctb], Davide Risso [ctb, fnd], Lieven Clement [ctb, fnd]
Maintainer: Alexandre Segers <alexandresegers at outlook.com>
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 1.2.0, https://bioconductor.org/packages/omicsGMF.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("omicsGMF")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("omicsGMF")| Proteomics-vignette: omicsGMF | HTML | R Script |
| RNASeq-vignette: omicsGMF | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, DimensionReduction, GeneExpression, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0), sgdGMF, SingleCellExperiment, scuttle, scater |
| Imports | stats, utils, Matrix, S4Vectors, SummarizedExperiment, DelayedArray, MatrixGenerics, BiocSingular, BiocParallel, beachmat, ggplot2, methods, QFeatures |
| System Requirements | |
| URL | https://github.com/statOmics/omicsGMF |
| Bug Reports | https://github.com/statOmics/omicsGMF/issues |
See More
| Suggests | knitr, dplyr, testthat, BiocGenerics, BiocStyle, graphics, grDevices |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | omicsGMF_1.2.0.tar.gz |
| Windows Binary (x86_64) | omicsGMF_1.2.0.zip |
| macOS Binary (big-sur-x86_64) | omicsGMF_1.2.0.tgz |
| macOS Binary (sonoma-arm64) | omicsGMF_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/omicsGMF |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/omicsGMF |
| Package Short Url | https://bioconductor.org/packages/omicsGMF/ |
| Package Downloads Report | Download Stats |