bHIVE
This is the development version of bHIVE; to use it, please install the devel version of Bioconductor.
B-cell Hybrid Immune Variant Engine
Bioconductor version: Development (3.24)
bHIVE implements an artificial immune network (AI-Net) for clustering and classification of high-dimensional data such as mass cytometry and single-cell profiles. A population of prototypes, called antibodies, evolves by clonal selection, somatic hypermutation and network suppression, and the learned prototypes summarize cell populations in the original marker units. The same fitted model clusters a dataset and labels new cells. bHIVE accepts SummarizedExperiment and SingleCellExperiment objects and integrates with bluster through bHIVEParam. A C++ backend computes affinities, mutations and suppression, and optional R6 modules add mechanisms such as germinal center selection, microenvironment-dependent mutation and isotype switching. The package also provides multilayer clustering, grid search and caret model wrappers.
Author: Nick Borcherding [aut, cre] 
Maintainer: Nick Borcherding <ncborch at gmail.com>
citation("bHIVE")):Nick Borcherding. bHIVE: B-cell Hybrid Immune Variant Engine. doi:10.18129/B9.bioc.bHIVE, R package version 0.99.8, https://bioconductor.org/packages/bHIVE.
Generated from the package metadata; it may differ from the package's own citation.
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("bHIVE")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("bHIVE")| Composing immune modules with AINet | HTML |
| Immune-inspired prototypes for cytometry and single-cell data with bHIVE | HTML |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | CellBasedAssays, Classification, Clustering, FlowCytometry, Network, SingleCell, Software |
| Version | 0.99.8 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | BiocParallel, bluster, cluster, clusterCrit, ggplot2 (>= 3.4.0), methods, R6, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment |
| System Requirements | |
| URL | https://www.borch.dev/uploads/bhive/ |
| Bug Reports | https://github.com/BorchLab/bHIVE/issues |
See More
| Suggests | BiocStyle, caret, FlowSOM, HDCytoData, knitr, rmarkdown, Rtsne, spelling, testthat (>= 3.0.0), umap |
| Linking To | Rcpp, RcppArmadillo |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/bHIVE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/bHIVE |
| Package Short Url | https://bioconductor.org/packages/bHIVE/ |
| Package Downloads Report | Download Stats |