Package: SingleCellAlleleExperiment 1.3.0

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_1.3.0.tar.gz
SingleCellAlleleExperiment_1.3.0.zip(r-4.5)SingleCellAlleleExperiment_1.3.0.zip(r-4.4)SingleCellAlleleExperiment_1.1.0.zip(r-4.3)
SingleCellAlleleExperiment_1.3.0.tgz(r-4.4-any)SingleCellAlleleExperiment_1.1.0.tgz(r-4.3-any)
SingleCellAlleleExperiment_1.3.0.tar.gz(r-4.5-noble)SingleCellAlleleExperiment_1.3.0.tar.gz(r-4.4-noble)
SingleCellAlleleExperiment_1.3.0.tgz(r-4.4-emscripten)SingleCellAlleleExperiment_1.1.0.tgz(r-4.3-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'))

Peer review:

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

6.26 score 6 stars 5 scripts 173 downloads 5 exports 38 dependencies

Last updated 23 days agofrom:cdd2082152. Checks:OK: 2 NOTE: 1 ERROR: 2 WARNING: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxNOTEOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winERRORSep 16 2024
R-4.3-macERRORSep 16 2024

Exports:read_allele_countsrowData<-scae_subsetshowSingleCellAlleleExperiment

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelcodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSingleCellExperimentsnowSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc

An introduction to the SingleCellAlleleExperiment class

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

Rendered fromscae_intro.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-10-22
Started: 2024-03-07