Ibex
This is the development version of Ibex; for the stable release version, see Ibex.
Methods for BCR single-cell embedding
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.3.1 |
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Ibex_1.3.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | Ibex_1.3.1.tgz |
| macOS Binary (sonoma-arm64) | Ibex_1.3.1.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 |