Package: Ibex
Title: Methods for BCR single-cell embedding
Version: 1.1.1
Authors@R: c(
    person(given = "Nick", family = "Borcherding", role = c("aut", "cre", "cph"), email = "ncborch@gmail.com"),
	person(given = "Qile", family = "Yang", role = "ctb", email = "qile.yang@berkeley.edu", comment = c(ORCID = "0009-0005-0148-2499")))
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: 7.3.3
biocViews: Software, ImmunoOncology, SingleCell, Classification,
        Annotation, Sequencing
Depends: R (>= 4.4.0)
Imports: basilisk, immApex (>= 1.3.2), methods, Matrix, reticulate (>=
        1.43.0), SeuratObject, scRepertoire, SingleCellExperiment,
        stats, SummarizedExperiment, tensorflow, tools
Suggests: basilisk.utils, BiocStyle, bluster, dplyr, ggplot2,
        kableExtra, knitr, lifecycle, 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.r-universe.dev
Date/Publication: 2026-04-03 15:00:27 UTC
RemoteUrl: https://github.com/bioc/Ibex
RemoteRef: HEAD
RemoteSha: 38bb71dc9ed0a983b1d6d4118e31d46e2d8653e3
NeedsCompilation: no
Packaged: 2026-04-04 06:12:35 UTC; root
Author: Nick Borcherding [aut, cre, cph],
  Qile Yang [ctb] (ORCID: <https://orcid.org/0009-0005-0148-2499>)
Maintainer: Nick Borcherding <ncborch@gmail.com>
Built: R 4.6.0; ; 2026-04-04 06:15:05 UTC; unix
