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-1.3.0(bioc 3.21)SingleCellAlleleExperiment-1.2.0(bioc 3.20)

datarepresentationinfrastructuresinglecelltranscriptomicsgeneexpressiongeneticsimmunooncologydataimport

6.34 score 7 stars 12 scripts 168 downloads 5 exports 38 dependencies

Last updated 24 days agofrom:8b0584dc36. Checks:3 OK, 2 NOTE, 1 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 28 2025
R-4.5-winNOTEJan 28 2025
R-4.5-macWARNINGJan 28 2025
R-4.5-linuxNOTEJan 28 2025
R-4.4-winOKJan 28 2025
R-4.4-macOKJan 28 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 Jan 28 2025.

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