Package: VAExprs
Type: Package
Title: Generating Samples of Gene Expression Data with Variational
        Autoencoders
Description: 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.
Version: 1.18.0
Date: 2022-05-16
Authors@R: c(person(given="Dongmin", family="Jung", email="dmdmjung@gmail.com", role=c("cre", "aut"), comment = c(ORCID = "0000-0001-7499-8422")))
Depends: keras, mclust
Imports: SingleCellExperiment, SummarizedExperiment, tensorflow,
        scater, CatEncoders, DeepPINCS, purrr, DiagrammeR, stats
Suggests: SC3, knitr, testthat, reticulate, rmarkdown
License: Artistic-2.0
biocViews: Software, GeneExpression, SingleCell
NeedsCompilation: no
VignetteBuilder: knitr
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libglpk-dev make
        libharfbuzz-dev default-jdk libicu-dev libjpeg-dev libpng-dev
        libtiff-dev libuv1-dev libwebp-dev libxml2-dev libssl-dev
        python3 libx11-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:56:36 UTC
RemoteUrl: https://github.com/bioc/VAExprs
RemoteRef: RELEASE_3_23
RemoteSha: 225150fc2060966171795cd9b6c742c7b94723a3
Packaged: 2026-04-30 07:03:44 UTC; root
Author: Dongmin Jung [cre, aut] (ORCID:
    <https://orcid.org/0000-0001-7499-8422>)
Maintainer: Dongmin Jung <dmdmjung@gmail.com>
Built: R 4.6.0; ; 2026-04-30 07:12:28 UTC; windows
