Package: Ibex 1.2.0

Nick Borcherding

Ibex: Methods for BCR single-cell embedding

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.

Authors:Nick Borcherding [aut, cre, cph], Qile Yang [ctb]

Ibex_1.2.0.tar.gz
Ibex_1.2.0.zip(r-4.7-any)Ibex_1.2.0.zip(r-4.6-any)Ibex_1.2.0.zip(r-4.5-any)
Ibex_1.2.0.tgz(r-4.6-any)Ibex_1.2.0.tgz(r-4.5-any)
Ibex_1.2.0.tar.gz(r-4.7-any)Ibex_1.2.0.tar.gz(r-4.6-any)
Ibex_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Ibex/json (API)

# Install 'Ibex' in R:

install.packages('Ibex', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/borchlab/ibex/issues

Datasets:

ibex_example - A SingleCellExperiment object with 200 randomly-sampled B cells with BCR sequences from the 10x Genomics 2k_BEAM-Ab_Mouse_HEL_5pv2 dataset.
ibex_vdj - Full filtered_annotated_contig.csv from the 10x 2k_BEAM-Ab_Mouse_HEL_5pv2

On BioConductor:Ibex-1.3.1(bioc 3.24)Ibex-1.2.0(bioc 3.23)

software immunooncology singlecell classification annotation sequencing

6.73 score 28 stars 32 scripts 234 downloads 4 exports 124 dependencies

Last updated from:222b168899 (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	257
linux-devel	NOTE	1162
source / vignettes	OK	924
linux-release	NOTE	1131
macos-release	NOTE	1135
macos-oldrel	NOTE	1168
windows-devel	NOTE	570
windows-release	NOTE	580
windows-oldrel	NOTE	615
wasm-release	OK	141

Exports:combineExpandedBCR CoNGAfy Ibex_matrix runIbex

Dependencies:abind askpass backports base64enc basilisk Biobase BiocGenerics Biostrings cachem cli codetools config cpp11 crayon curl DelayedArray digest dir.expiry dotCall64 dplyr evmix farver fastmap filelock future future.apply generics GenomicRanges ggalluvial ggdendro ggforce ggplot2 ggraph ggrepel globals glue graphlayouts gridExtra gsl gtable here httr igraph immApex immReferent iNEXT IRanges isoband jsonlite labeling lattice lazyeval lifecycle listenv magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mime openssl parallelly pillar pkgconfig plyr png polyclip processx progressr ps purrr quantreg R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RcppTOML reshape2 reticulate rjson rlang rprojroot rstudioapi rvest S4Arrays S4Vectors S7 scales scRepertoire selectr Seqinfo SeuratObject SingleCellExperiment sp spam SparseArray SparseM stringi stringr SummarizedExperiment survival sys systemfonts tensorflow tfautograph tfruns tibble tidygraph tidyr tidyselect tweenr utf8 vctrs viridis viridisLite whisker withr xml2 XVector yaml

A tour of Ibex.

Rendered fromIbex.Rmdusingknitr::knitr

Last update: 2025-09-23
Started: 2025-02-09

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Ibex: Methods for BCR single-cell embedding	Ibex-package Ibex
combineBCR for CDR1/2/3 sequences	combineExpandedBCR
Reduce a Single-Cell Object to Representative Cells	CoNGAfy
Filter Single-Cell Data Based on CDR3 Sequences	filter.cells
A SingleCellExperiment object with 200 randomly-sampled B cells with BCR sequences from the 10x Genomics 2k_BEAM-Ab_Mouse_HEL_5pv2 dataset.	ibex_example
Ibex Matrix Interface	Ibex_matrix
Full filtered_annotated_contig.csv from the 10x 2k_BEAM-Ab_Mouse_HEL_5pv2	ibex_vdj
Ibex Single-Cell Calculation	runIbex