Package: Ibex 1.3.1

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_1.3.1.tar.gz
Ibex_1.3.1.zip(r-4.7)Ibex_1.3.1.zip(r-4.6)Ibex_1.3.1.zip(r-4.5)
Ibex_1.3.1.tgz(r-4.6-any)Ibex_1.3.1.tgz(r-4.5-any)
Ibex_1.3.1.tar.gz(r-4.7-any)Ibex_1.3.1.tar.gz(r-4.6-any)
Ibex_1.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Ibex/json (API)
NEWS

# Install 'Ibex' in R:
install.packages('Ibex', repos = c('https://bioc.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-1.3.0(bioc 3.24)Ibex-1.2.0(bioc 3.23)

softwareimmunooncologysinglecellclassificationannotationsequencing

6.95 score 27 stars 17 scripts 182 downloads 4 exports 124 dependencies

Last updated from:e9edf77606. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE206
linux-devel-x86_64NOTE1075
source / vignettesOK857
linux-release-x86_64NOTE1025
macos-release-arm64NOTE1125
macos-oldrel-arm64NOTE1056
windows-develNOTE662
windows-releaseNOTE596
windows-oldrelNOTE630
wasm-releaseOK168

Exports:combineExpandedBCRCoNGAfyIbex_matrixrunIbex

Dependencies:abindaskpassbackportsbase64encbasiliskBiobaseBiocGenericsBiostringscachemclicodetoolsconfigcpp11crayoncurlDelayedArraydigestdir.expirydotCall64dplyrevmixfarverfastmapfilelockfuturefuture.applygenericsGenomicRangesggalluvialggdendroggforceggplot2ggraphggrepelglobalsgluegraphlayoutsgridExtragslgtableherehttrigraphimmApeximmReferentiNEXTIRangesisobandjsonlitelabelinglatticelazyevallifecyclelistenvmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemimeopensslparallellypillarpkgconfigplyrpngpolyclipprocessxprogressrpspurrrquantregR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppTOMLreshape2reticulaterjsonrlangrprojrootrstudioapirvestS4ArraysS4VectorsS7scalesscRepertoireselectrSeqinfoSeuratObjectSingleCellExperimentspspamSparseArraySparseMstringistringrSummarizedExperimentsurvivalsyssystemfontstensorflowtfautographtfrunstibbletidygraphtidyrtidyselecttweenrutf8vctrsviridisviridisLitewhiskerwithrxml2XVectoryaml

A tour of Ibex.

Nick Borcherding

Rendered fromIbex.Rmdusingknitr::knitron May 29 2026.

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