Package: bHIVE
Title: B-cell Hybrid Immune Variant Engine
Version: 0.99.8
Authors@R: c(
    person(given = "Nick", family = "Borcherding", role = c("aut", "cre"),
           email = "ncborch@gmail.com",
           comment = c(ORCID = "0000-0003-1427-6342")))
Description: bHIVE implements an artificial immune network (AI-Net) for
    clustering and classification of high-dimensional data such as mass
    cytometry and single-cell profiles. A population of prototypes, called
    antibodies, evolves by clonal selection, somatic hypermutation and network
    suppression, and the learned prototypes summarize cell populations in the
    original marker units. The same fitted model clusters a dataset and labels
    new cells. bHIVE accepts SummarizedExperiment and SingleCellExperiment
    objects and integrates with bluster through bHIVEParam. A C++ backend
    computes affinities, mutations and suppression, and optional R6 modules
    add mechanisms such as germinal center selection,
    microenvironment-dependent mutation and isotype switching. The package
    also provides multilayer clustering, grid search and caret model
    wrappers.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.3
biocViews: Software, Clustering, Classification, SingleCell,
        FlowCytometry, CellBasedAssays, Network
Depends: R (>= 4.5.0)
Imports: BiocParallel, bluster, cluster, clusterCrit, ggplot2 (>=
        3.4.0), methods, R6, Rcpp, S4Vectors, SingleCellExperiment,
        stats, SummarizedExperiment
LinkingTo: Rcpp, RcppArmadillo
Suggests: BiocStyle, caret, FlowSOM, HDCytoData, knitr, rmarkdown,
        Rtsne, spelling, testthat (>= 3.0.0), umap
VignetteBuilder: knitr
Config/testthat/edition: 3
Language: en-US
URL: https://www.borch.dev/uploads/bhive/
BugReports: https://github.com/BorchLab/bHIVE/issues
git_url: https://git.bioconductor.org/packages/bHIVE
git_branch: devel
git_last_commit: bcab3c8
git_last_commit_date: 2026-10-16
Repository: Bioconductor 3.24
Date/Publication: 2026-11-08
NeedsCompilation: yes
Packaged: 2026-11-08 21:45:11 UTC; biocbuild
Author: Nick Borcherding [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1427-6342>)
Maintainer: Nick Borcherding <ncborch@gmail.com>
