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
Config/pak/sysreqs: libglpk-dev libxml2-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-16 18:55:33 UTC
RemoteUrl: https://github.com/BiocStaging/bHIVE
RemoteRef: HEAD
RemoteSha: bcab3c85a0ef081a6c9831d84fd73659fe4eae8d
NeedsCompilation: yes
Packaged: 2026-10-16 21:32:19 UTC; root
Author: Nick Borcherding [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1427-6342>)
Maintainer: Nick Borcherding <ncborch@gmail.com>