Package: Ibex
Title: Methods for BCR single-cell embedding
Version: 0.99.34
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 (>= 4.5.0)
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)
git_url: https://git.bioconductor.org/packages/Ibex
git_branch: devel
git_last_commit: 124a6b3
git_last_commit_date: 2025-10-16
Repository: Bioconductor 3.22
Date/Publication: 2025-10-17
NeedsCompilation: no
Packaged: 2025-10-17 22:10:15 UTC; biocbuild
Author: Nick Borcherding [aut, cre]
Maintainer: Nick Borcherding <ncborch@gmail.com>
