Package: SingleCellAlleleExperiment 1.3.1
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:
SingleCellAlleleExperiment_1.3.1.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_1.3.1.tgz(r-4.4-any)SingleCellAlleleExperiment_1.1.0.tgz(r-4.3-any)
SingleCellAlleleExperiment_1.3.1.tar.gz(r-4.5-noble)SingleCellAlleleExperiment_1.3.1.tar.gz(r-4.4-noble)
SingleCellAlleleExperiment_1.3.1.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')) |
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
Last updated 2 days agofrom:e6fe9a5a36. Checks:ERROR: 3 WARNING: 2 NOTE: 1 OK: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Dec 22 2024 |
| R-4.5-win | NOTE | Nov 30 2024 |
| R-4.5-linux | WARNING | Dec 22 2024 |
| R-4.4-win | OK | Nov 30 2024 |
| R-4.4-mac | WARNING | Dec 22 2024 |
| R-4.3-win | ERROR | Sep 16 2024 |
| R-4.3-mac | ERROR | Sep 16 2024 |
Exports:read_allele_countsrowData<-scae_subsetshowSingleCellAlleleExperiment
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelcodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSingleCellExperimentsnowSparseArraySummarizedExperimentsysUCSC.utilsXVector
