Package: Ibex
Title: Methods for BCR single-cell embedding
Version: 1.0.0
Authors@R: c(
    person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "ncborch@gmail.com"))
Description: Implementation of the Ibex algorithm for single-cell
        embedding based on BCR sequences. The package includes a
        standalone function to encode BCR sequence information by amino
        acid properties or sequence order using tensorflow-based
        autoencoder. In addition, the package interacts with
        SingleCellExperiment or Seurat data objects.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.2
biocViews: Software, ImmunoOncology, SingleCell, Classification,
        Annotation, Sequencing
Depends: R (>= 4.4.0)
Imports: basilisk, immApex (>= 1.3.2), methods, Matrix, reticulate (>=
        1.43.0), rlang, SeuratObject, scRepertoire,
        SingleCellExperiment, stats, SummarizedExperiment, tensorflow,
        tools
Suggests: basilisk.utils, BiocStyle, bluster, dplyr, ggplot2,
        kableExtra, knitr, markdown, mumosa, patchwork, Peptides,
        rmarkdown, scater, spelling, testthat (>= 3.0.0), utils,
        viridis
SystemRequirements: Python (via basilisk)
VignetteBuilder: knitr
Language: en-US
URL: https://github.com/BorchLab/Ibex/
BugReports: https://github.com/BorchLab/Ibex/issues
Roxygen: list(markdown = TRUE)
Config/pak/sysreqs: libfontconfig1-dev libfreetype6-dev libglpk-dev
        libgsl0-dev libicu-dev libpng-dev libxml2-dev libssl-dev
        python3 zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:38:26 UTC
RemoteUrl: https://github.com/bioc/Ibex
RemoteRef: RELEASE_3_22
RemoteSha: 92396daeb0b512d50a3fa8988fd6e014395ffe52
NeedsCompilation: no
Packaged: 2026-03-04 09:03:33 UTC; root
Author: Nick Borcherding [aut, cre]
Maintainer: Nick Borcherding <ncborch@gmail.com>
Built: R 4.5.2; ; 2026-03-04 09:06:29 UTC; windows
