VAExprs
This is the development version of VAExprs; for the stable release version, see VAExprs.
Generating Samples of Gene Expression Data with Variational Autoencoders
Bioconductor version: Development (3.21)
A fundamental problem in biomedical research is the low number of observations, mostly due to a lack of available biosamples, prohibitive costs, or ethical reasons. By augmenting a few real observations with artificially generated samples, their analysis could lead to more robust and higher reproducible. One possible solution to the problem is the use of generative models, which are statistical models of data that attempt to capture the entire probability distribution from the observations. Using the variational autoencoder (VAE), a well-known deep generative model, this package is aimed to generate samples with gene expression data, especially for single-cell RNA-seq data. Furthermore, the VAE can use conditioning to produce specific cell types or subpopulations. The conditional VAE (CVAE) allows us to create targeted samples rather than completely random ones.
Author: Dongmin Jung [cre, aut] (ORCID:
Maintainer: Dongmin Jung <dmdmjung at gmail.com>
citation("VAExprs")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("VAExprs")
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("VAExprs")| VAExprs | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, SingleCell, Software |
| Version | 1.13.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 years) |
| License | Artistic-2.0 |
| Depends | keras, mclust |
| Imports | SingleCellExperiment, SummarizedExperiment, tensorflow, scater, CatEncoders, DeepPINCS, purrr, DiagrammeR, stats |
| System Requirements | |
| URL |
See More
| Suggests | SC3, knitr, testthat, reticulate, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | GenProSeq |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | VAExprs_1.13.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/VAExprs |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/VAExprs |
| Bioc Package Browser | https://code.bioconductor.org/browse/VAExprs/ |
| Package Short Url | https://bioconductor.org/packages/VAExprs/ |
| Package Downloads Report | Download Stats |