Package: geneticumap
Title: Evolutionary Algorithm for UMAP-based Clustering Pipeline
        Parameter Optimization for Single-Cell RNA-Seq Data
Version: 0.99.3
Date: 2026-10-13
Authors@R: c(
    person("Lisa-Maria", "Winter", email = "lisa-maria-1.winter@uni-ulm.de", role = c("aut")),
    person("Hanna", "Wagner", email = "hanna.wagner@uni-ulm.de", role = c("aut")),
    person("Dominik", "Dreiheller", role = c("aut")),
    person("Hans A.", "Kestler", email = "hans.kestler@uni-ulm.de", role = c("cre"), comment=c(ORCID="0000-0002-4759-5254")))
Description: The geneticumap package searches for single-cell
        clustering parameters by treating the Seurat preprocessing and
        clustering workflow as an optimization problem. The UMAP-based
        clustering pipeline parameters for single-cell RNA-seq data
        (like resolution, number of PCs, or neighbor counts) evolve
        using an evolutionary algorithm to systematically search for an
        optimal set of parameters for a given dataset. The most
        appropriate configuration is objectively identified by the
        Calinski-Harabasz index. The package is developed at the
        [Institute of Medical Systems Biology of Ulm
        University](https://sysbio.uni-ulm.de).
License: MIT + file LICENSE
Depends: R (>= 4.5.0)
Imports: ecr, clusterCrit, Seurat, BBmisc, checkmate, SeuratObject,
        jsonlite, parallelMap, plotly, ggplot2, parallelly
Suggests: hdf5r, testthat (>= 3.0.0), knitr, rmarkdown, htmlwidgets
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Config/testthat/edition: 3
VignetteBuilder: knitr
biocViews: GeneExpression, SingleCell, Transcriptomics, Clustering,
        DimensionReduction, Preprocessing
URL: https://github.com/sysbio-bioinf/geneticumap
BugReports: https://github.com/sysbio-bioinf/geneticumap/issues
Config/roxygen2/version: 8.1.1
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev libglpk-dev libglu1-mesa-dev make
        libharfbuzz-dev texlive libicu-dev libpng-dev libuv1-dev
        libxml2-dev libgl1-mesa-dev libssl-dev python3 zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-13 10:35:45 UTC
RemoteUrl: https://github.com/BiocStaging/geneticumap
RemoteRef: HEAD
RemoteSha: 717508293cf3311b3135a65e05e9e1cbcc6c0bb8
NeedsCompilation: no
Packaged: 2026-10-13 12:08:40 UTC; root
Author: Lisa-Maria Winter [aut],
  Hanna Wagner [aut],
  Dominik Dreiheller [aut],
  Hans A. Kestler [cre] (ORCID: <https://orcid.org/0000-0002-4759-5254>)
Maintainer: Hans A. Kestler <hans.kestler@uni-ulm.de>