Package: Ibex
Title: Methods for BCR single-cell embedding 
Version: 1.1.0
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 (>= 4.5.0)
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: 1dadb52
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
