Ibex
This is the released version of Ibex; for the devel version, see Ibex.
Methods for BCR single-cell embedding
Bioconductor version: Release (3.23)
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.
Author: Nick Borcherding [aut, cre, cph], Qile Yang [ctb] 
Maintainer: Nick Borcherding <ncborch at gmail.com>
citation("Ibex")):Nick Borcherding. Ibex: Methods for BCR single-cell embedding. doi:10.18129/B9.bioc.Ibex, R package version 1.2.0, https://bioconductor.org/packages/Ibex.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Ibex")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("Ibex")| Charging through Ibex | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Annotation, Classification, ImmunoOncology, Sequencing, SingleCell, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | basilisk, immApex (>= 1.3.2), methods, Matrix, reticulate (>= 1.43.0), SeuratObject, scRepertoire, SingleCellExperiment, stats, SummarizedExperiment, tensorflow, tools |
| System Requirements | Python (via basilisk) |
| URL | https://github.com/BorchLab/Ibex/ |
| Bug Reports | https://github.com/BorchLab/Ibex/issues |
See More
| Suggests | basilisk.utils, BiocStyle, bluster, dplyr, ggplot2, kableExtra, knitr, lifecycle, markdown, mumosa, patchwork, Peptides, rmarkdown, scater, spelling, testthat (>= 3.0.0), utils, viridis |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Ibex_1.2.0.tar.gz |
| Windows Binary (x86_64) | Ibex_1.2.0.zip |
| macOS Binary (big-sur-x86_64) | Ibex_1.2.0.tgz |
| macOS Binary (sonoma-arm64) | Ibex_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Ibex |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Ibex |
| Package Short Url | https://bioconductor.org/packages/Ibex/ |
| Package Downloads Report | Download Stats |