{ "_id": "6ad9d7c8021a938ed758ecc8", "Package": "VAExprs", "Type": "Package", "Title": "Generating Samples of Gene Expression Data with Variational\nAutoencoders", "Description": "A fundamental problem in biomedical research is the low\nnumber of observations, mostly due to a lack of available\nbiosamples, prohibitive costs, or ethical reasons. By\naugmenting a few real observations with artificially generated\nsamples, their analysis could lead to more robust and higher\nreproducible. One possible solution to the problem is the use\nof generative models, which are statistical models of data that\nattempt to capture the entire probability distribution from the\nobservations. Using the variational autoencoder (VAE), a\nwell-known deep generative model, this package is aimed to\ngenerate samples with gene expression data, especially for\nsingle-cell RNA-seq data. Furthermore, the VAE can use\nconditioning to produce specific cell types or subpopulations.\nThe conditional VAE (CVAE) allows us to create targeted samples\nrather than completely random ones.", "Version": "1.19.0", "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\")))", "License": "Artistic-2.0", "biocViews": "Software, GeneExpression, SingleCell", "NeedsCompilation": "no", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libglpk-dev make default-jdk libicu-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev python3 libx11-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:56:36 UTC", "RemoteUrl": "https://github.com/bioc/VAExprs", "RemoteRef": "HEAD", "RemoteSha": "9b454e94a58664631eabaefd9f2d0efd0ed0de7b", "Packaged": { "Date": "2026-10-22 09:20:08 UTC", "User": "root" }, "Author": "Dongmin Jung [cre, aut] (ORCID:\n)", "Maintainer": "Dongmin Jung ", "_user": "bioc", "_type": "src", "_file": "VAExprs_1.19.0.tar.gz", "_fileid": "https://r2.ropensci.org/9ba93053f37139677f0319613c043906a2da4a758b1cacca7aec22e86ea49e0b", "_filesize": 493709, "_sha256": "9ba93053f37139677f0319613c043906a2da4a758b1cacca7aec22e86ea49e0b", "_expires": "2027-01-30T09:30:46.000Z", "_created": "2026-10-22T09:20:08.000Z", "_published": "2026-10-22T09:30:48.146Z", "_upstream": "https://github.com/bioc/VAExprs", "_status": "success", "_maintainer": { "name": "Dongmin Jung", "email": "dmdmjung@gmail.com", "login": "dongminjung", "description": "", "uuid": 25045090, "orcid": "0000-0001-7499-8422" }, "_jobs": [ { "job": 119743700305, "time": 225, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "12415441687" }, { "job": 119743700216, "time": 506, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12415172732" }, { "job": 119743700278, "time": 568, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12415139485" }, { "job": 119743700199, "time": 325, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "12415952294" }, { "job": 119743700337, "time": 267, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "12414818580" }, { "job": 119740585283, "time": 423, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12414892379" }, { "job": 119743700121, "time": 186, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12414833133" }, { "job": 119743700145, "time": 360, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12415377285" }, { "job": 119743700172, "time": 322, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "12415206982" }, { "job": 119743700286, "time": 351, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12414989275" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39753746829", "_commit": { "id": "9b454e94a58664631eabaefd9f2d0efd0ed0de7b", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380996 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "keras", "role": "Depends" }, { "package": "mclust", "role": "Depends" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "tensorflow", "role": "Imports" }, { "package": "scater", "role": "Imports" }, { "package": "CatEncoders", "role": "Imports" }, { "package": "DeepPINCS", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "DiagrammeR", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "SC3", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "reticulate", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.19.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.18.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "software", "geneexpression", "singlecell", "openjdk" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 479, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 447, "source": "https://www.bioconductor.org/packages/stats/bioc/VAExprs" }, "_searchresults": 4, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/VAExprs.html" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "fit_vae", "gen_exprs", "plot_aug", "plot_vae" ], "_help": [ { "page": "fit_vae", "title": "Variational autoencoder model fitting", "topics": [ "fit_vae" ] }, { "page": "gen_exprs", "title": "Generate samples with expression data", "topics": [ "gen_exprs" ] }, { "page": "plot_aug", "title": "Visualization for augmented data", "topics": [ "plot_aug" ] }, { "page": "plot_vae", "title": "Visualization for the variational autoencoder", "topics": [ "plot_vae" ] } ], "_readme": "https://github.com/bioc/VAExprs/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "assorthead", "backports", "base64enc", "beachmat", "beeswarm", "BH", "Biobase", "BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "bit", "bit64", "blob", "bslib", "cachem", "CatEncoders", "cli", "clipr", "codetools", "config", "cpp11", "crayon", "curl", "data.table", "data.tree", "DBI", "DeepPINCS", "DelayedArray", "DiagrammeR", "digest", "dplyr", "dqrng", "dtt", "english", "evaluate", "farver", "fastmap", "fastmatch", "fingerprint", "float", "FNN", "fontawesome", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggbeeswarm", "ggplot2", "ggrepel", "glue", "gridExtra", "gtable", "here", "highr", "hms", "hoardr", "htmltools", "htmlwidgets", "httr", "hunspell", "igraph", "IRanges", "irlba", "isoband", "ISOcodes", "iterators", "itertools", "jquerylib", "jsonlite", "keras", "knitr", "koRpus", "koRpus.lang.en", "labeling", "lambda.r", "lattice", "lexicon", "lgr", "lifecycle", "magrittr", "matlab", "Matrix", "MatrixExtra", "MatrixGenerics", "matrixStats", "mclust", "memoise", "mgsub", "mime", "mlapi", "NLP", "openssl", "pheatmap", "pillar", "pkgconfig", "png", "prettyunits", "processx", "progress", "PRROC", "ps", "purrr", "qdapRegex", "quanteda", "R6", "rappdirs", "rcdk", "rcdklibs", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppML", "RcppProgress", "RcppTOML", "readr", "reticulate", "RhpcBLASctl", "rJava", "rlang", "rmarkdown", "rprojroot", "rsparse", "RSpectra", "RSQLite", "rstudioapi", "rsvd", "Rtsne", "rvest", "S4Arrays", "S4Vectors", "S7", "sass", "ScaledMatrix", "scales", "scater", "scuttle", "selectr", "Seqinfo", "SingleCellExperiment", "sitmo", "slam", "snow", "SnowballC", "SparseArray", "stopwords", "stringdist", "stringi", "stringr", "SummarizedExperiment", "sylly", "sylly.en", "sys", "syuzhet", "tensorflow", "text2vec", "textclean", "textshape", "textstem", "tfautograph", "tfruns", "tibble", "tidyr", "tidyselect", "tinytex", "tm", "tokenizers", "ttgsea", "tzdb", "utf8", "uwot", "vctrs", "vipor", "viridis", "viridisLite", "visNetwork", "vroom", "webchem", "whisker", "withr", "xfun", "xml2", "XVector", "yaml", "zeallot", "zoo" ], "_sysdeps": [ { "shlib": "libjvm", "package": "openjdk-25-jre-headless", "headers": "openjdk-25-jre-headless", "source": "openjdk", "version": "25.0.4.1+1-1~26.04.4", "name": "openjdk", "homepage": "https://openjdk.java.net/", "description": "OpenJDK Java runtime, using Hotspot JIT (headless)" } ], "_vignettes": [ { "source": "VAExprs.Rmd", "filename": "VAExprs.html", "title": "Generating Samples of Gene Expression Data with Variational Autoencoders", "author": "Dongmin Jung", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Example", "VAE", "CVAE", "Session information", "References" ], "created": "2021-06-07 13:40:03", "modified": "2021-12-15 00:12:09", "commits": 8 } ], "_score": 4, "_indexed": true, "_nocasepkg": "vaexprs", "_universes": [ "bioc", "dongminjung" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.19.0", "date": "2026-10-22T09:25:56.000Z", "distro": "resolute", "commit": "9b454e94a58664631eabaefd9f2d0efd0ed0de7b", "fileid": "https://r2.ropensci.org/0bcaf53cdee482f48ac7e33e0de1484def20bb4e6be9a650fc910dfb777ffcee", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39753746829" }, { "r": "4.6.1", "os": "linux", "version": "1.19.0", "date": "2026-10-22T09:27:18.000Z", "distro": "resolute", "commit": "9b454e94a58664631eabaefd9f2d0efd0ed0de7b", "fileid": "https://r2.ropensci.org/7ce94f3a30623af2d7bcc69803a4bf39bc7ac8ba6b8345aefb311caaf981b79b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39753746829" }, { "r": "4.5.3", "os": "mac", "version": "1.19.0", "date": "2026-10-22T09:23:14.000Z", "commit": "9b454e94a58664631eabaefd9f2d0efd0ed0de7b", "fileid": "https://r2.ropensci.org/209b9fdc05d74070d4ca744d4bfe217230cbd3a261ee5465e7908bc5fc5bc1a5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39753746829" }, { "r": "4.6.1", "os": "mac", "version": "1.19.0", "date": "2026-10-22T09:23:35.000Z", "commit": "9b454e94a58664631eabaefd9f2d0efd0ed0de7b", "fileid": "https://r2.ropensci.org/99a6147a7c7767d966c5b92fa6ed61ee821e43f5bfd5d35d538f7359615ca633", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39753746829" }, { "r": "4.6.0", "os": "wasm", "version": "1.19.0", "date": "2026-10-22T09:23:51.000Z", "commit": "9b454e94a58664631eabaefd9f2d0efd0ed0de7b", "fileid": "https://r2.ropensci.org/975eab779b34a242b9e0556a0b76daa1a87776c2852cdae5db2f4b7e47f23f4c", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39753746829" }, { "r": "4.7.0", "os": "win", "version": "1.19.0", "date": "2026-10-22T09:22:21.000Z", "commit": "9b454e94a58664631eabaefd9f2d0efd0ed0de7b", "fileid": "https://r2.ropensci.org/5dc6469579d308c546f8bb87fa5b8c88096616c48bd6a22115fd07bafe467b44", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39753746829" }, { "r": "4.5.3", "os": "win", "version": "1.19.0", "date": "2026-10-22T09:22:14.000Z", "commit": "9b454e94a58664631eabaefd9f2d0efd0ed0de7b", "fileid": "https://r2.ropensci.org/0c24359c6cae66609b2aa16de180104948fe5982d968adab21557a115f82ddd0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39753746829" }, { "r": "4.6.1", "os": "win", "version": "1.19.0", "date": "2026-10-22T09:22:22.000Z", "commit": "9b454e94a58664631eabaefd9f2d0efd0ed0de7b", "fileid": "https://r2.ropensci.org/d9a2d443d672e05a800440b5c2193d23dd49abf8f683378073c9d273aae8ad82", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39753746829" } ] }