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: 1.16.0
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 libfontconfig1-dev libfreetype6-dev
        libfribidi-dev libglpk-dev make libharfbuzz-dev default-jdk
        libicu-dev libjpeg-dev libpng-dev libtiff-dev libwebp-dev
        libxml2-dev libssl-dev python3 libx11-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:11:03 UTC
RemoteUrl: https://github.com/bioc/VAExprs
RemoteRef: RELEASE_3_22
RemoteSha: 1b7ae7b8b2a114eca3d336ba347f79c66266cba0
Packaged: 2025-11-11 18:16:06 UTC; root
Author: Dongmin Jung [cre, aut] (ORCID:
    <https://orcid.org/0000-0001-7499-8422>)
Maintainer: Dongmin Jung <dmdmjung@gmail.com>
Built: R 4.5.2; ; 2025-11-11 18:22:24 UTC; windows
