Ibex
This is thereleased version of Ibex; for the devel version, seeIbex.
Methods for BCR single-cell embedding
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("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 appropriateBioconductor 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 | 1.0.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| License | MIT + fileLICENSE |
| 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 |
See More
| Suggests | basilisk.utils,BiocStyle,bluster,dplyr,ggplot2,kableExtra,knitr,markdown,mumosa,patchwork,Peptides,rmarkdown,scater,spelling,testthat (>= 3.0.0), utils,viridis |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation 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 |