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S4 Class for Single Cell Data with Allele and Functional Levels for Immune Genes

Bioconductor version: Release (3.19)

Defines a S4 class that is based on SingleCellExperiment. In addition to the usual gene layer the object can also store data for immune genes such as HLAs, Igs and KIRs at allele and functional level. The package is part of a workflow named single-cell ImmunoGenomic Diversity (scIGD), that firstly incorporates allele-aware quantification data for immune genes. This new data can then be used with the here implemented data structure and functionalities for further data handling and data analysis.

Author: Jonas Schuck [aut, cre] , Ahmad Al Ajami [aut] , Federico Marini [aut] , Katharina Imkeller [aut]

Maintainer: Jonas Schuck <jschuckdev at>

Citation (from within R, enter citation("SingleCellAlleleExperiment")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

An introduction to the SingleCellAlleleExperiment class HTML R Script
Reference Manual PDF


biocViews DataImport, DataRepresentation, GeneExpression, Genetics, ImmunoOncology, Infrastructure, SingleCell, Software, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.4.0), SingleCellExperiment
Imports SummarizedExperiment, BiocParallel, DelayedArray, methods, utils, Matrix, S4Vectors, stats
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Suggests scaeData, knitr, rmarkdown, BiocStyle, scran, scater, scuttle, ggplot2, patchwork,, AnnotationDbi, DropletUtils, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package SingleCellAlleleExperiment_1.0.0.tar.gz
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macOS Binary (x86_64) SingleCellAlleleExperiment_1.0.0.tgz
macOS Binary (arm64) SingleCellAlleleExperiment_1.0.0.tgz
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