Package: SingleCellAlleleExperiment 1.3.2

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_1.3.2.tar.gz
SingleCellAlleleExperiment_1.3.2.zip(r-4.5)SingleCellAlleleExperiment_1.3.2.zip(r-4.4)
SingleCellAlleleExperiment_1.3.2.tgz(r-4.5-any)SingleCellAlleleExperiment_1.3.2.tgz(r-4.4-any)
SingleCellAlleleExperiment_1.3.2.tar.gz(r-4.5-noble)SingleCellAlleleExperiment_1.3.2.tar.gz(r-4.4-noble)
SingleCellAlleleExperiment_1.3.2.tgz(r-4.4-emscripten)
SingleCellAlleleExperiment.pdf |SingleCellAlleleExperiment.html✨
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-1.3.2(bioc 3.21)SingleCellAlleleExperiment-1.2.0(bioc 3.20)

datarepresentationinfrastructuresinglecelltranscriptomicsgeneexpressiongeneticsimmunooncologydataimport

6.18 score 7 stars 12 scripts 169 downloads 5 exports 38 dependencies

Last updated 2 months agofrom:8b0584dc36. Checks:4 OK, 3 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 29 2025
R-4.5-winNOTEMar 29 2025
R-4.5-macNOTEMar 29 2025
R-4.5-linuxNOTEMar 29 2025
R-4.4-winOKMar 29 2025
R-4.4-macOKMar 29 2025
R-4.4-linuxOKMar 29 2025

Exports:read_allele_countsrowData<-scae_subsetshowSingleCellAlleleExperiment

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelcodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSingleCellExperimentsnowSparseArraySummarizedExperimentsysUCSC.utilsXVector

An introduction to the SingleCellAlleleExperiment class

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

Rendered fromscae_intro.Rmdusingknitr::rmarkdownon Mar 29 2025.

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