Ibex

This is the released version of Ibex; for the devel version, see Ibex.

Methods for BCR single-cell embedding

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DOI: 10.18129/B9.bioc.Ibex

Bioconductor version: Release (3.22)

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]

Maintainer: Nick Borcherding <ncborch at gmail.com>

Citation (from within R, enter citation("Ibex")):

Installation

To install this package, start R (version "4.5") 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 PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, Classification, ImmunoOncology, Sequencing, SingleCell, Software

Version 1.0.0

In Bioconductor since BioC 3.22 (R-4.5) (< 6 months)

License MIT + file LICENSE

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

System Requirements Python (via basilisk)

URL https://github.com/BorchLab/Ibex/

Bug Reports https://github.com/BorchLab/Ibex/issues

Suggests basilisk.utils, BiocStyle, bluster, dplyr, ggplot2, kableExtra, knitr, markdown, mumosa, patchwork, Peptides, rmarkdown, scater, spelling, testthat (>= 3.0.0), utils, viridis

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Ibex_1.0.0.tar.gz

Windows Binary (x86_64) Ibex_1.0.0.zip

macOS Binary (x86_64)

macOS Binary (arm64) Ibex_1.0.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/Ibex

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Ibex

Bioc Package Browser https://code.bioconductor.org/browse/Ibex/

Package Short Url https://bioconductor.org/packages/Ibex/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.22 Source Archive