Package: SingleCellAlleleExperiment 1.9.0

Jonas Schuck

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

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.

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

SingleCellAlleleExperiment_1.9.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
SingleCellAlleleExperiment/json (API)
NEWS

# Install 'SingleCellAlleleExperiment' in R:
install.packages('SingleCellAlleleExperiment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/agimkeller/singlecellalleleexperiment/issues

On BioConductor:SingleCellAlleleExperiment-1.9.0(bioc 3.24)SingleCellAlleleExperiment-1.8.0(bioc 3.23)

datarepresentationinfrastructuresinglecelltranscriptomicsgeneexpressiongeneticsimmunooncologydataimport

5.76 score 8 stars 12 scripts 260 downloads 5 exports 27 dependencies

Last updated from:9fb15ed615. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE209
linux-devel-x86_64WARNING484
source / vignettesOK484
linux-release-x86_64WARNING779
macos-release-arm64WARNING525
macos-oldrel-arm64WARNING1051
windows-develWARNING615
windows-releaseWARNING687
windows-oldrelWARNING739
wasm-releaseOK172

Exports:read_allele_countsrowData<-scae_subsetshowSingleCellAlleleExperiment

Dependencies:abindBHBiobaseBiocGenericsBiocParallelcodetoolscpp11DelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomicRangesIRangeslambda.rlatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfoSingleCellExperimentsnowSparseArraySummarizedExperimentXVector

An introduction to the SingleCellAlleleExperiment class

Jonas Schuck, Ahmad Al Ajami, Federico Marini, Katharina Imkeller

Rendered fromscae_intro.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-01-27
Started: 2024-03-07