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]

# 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)

datarepresentation infrastructure singlecell transcriptomics geneexpression genetics immunooncology dataimport

4.61 score 8 stars 17 scripts 402 downloads 5 exports 27 dependencies

Last updated from:9fb15ed615. Checks:1 NOTE, 8 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	192
linux-devel	ERROR	378
source / vignettes	ERROR	355
linux-release	ERROR	380
macos-release	ERROR	288
macos-oldrel	ERROR	200
windows-devel	ERROR	838
windows-release	ERROR	1013
windows-oldrel	ERROR	583
wasm-release	OK	162

Exports:read_allele_counts rowData<-scae_subset show SingleCellAlleleExperiment

Dependencies:abind BH Biobase BiocGenerics BiocParallel codetools cpp11 DelayedArray formatR futile.logger futile.options generics GenomicRanges IRanges lambda.r lattice Matrix MatrixGenerics matrixStats S4Arrays S4Vectors Seqinfo SingleCellExperiment snow SparseArray SummarizedExperiment XVector

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
Building first new subassay for SingleCellAllelexperiment object	alleles2genes
Check package installation for optional functionalities	check_valid_optional_package
Extend rowData with new annotation columns	ext_rd
Identify rows containing allele information	find_allele_ids
Building second new subassay for the SingleCellAlleleExperiment object	genes2functional
Get immune gene rows	get_agenes
Get Subassay with allele gene names and raw allele quantification	get_allelecounts
Knee plot info	get_knee_info
Get NCBI genes using the org.HS.db package	get_ncbi_org
Get non-immune rows	get_nigenes
Reading in allele quantification data into SingleCellAlleleExperiment object	read_allele_counts
Reading in allele-aware quantification data	read_from_sparse_allele
rowData setter for the SingleCellAlleleExperiment class	rowData<-,SingleCellAlleleExperiment,ANY-method
rowData-NULL-setter for the SingleCellAlleleExperiment class	rowData<-,SingleCellAlleleExperiment,NULL-method
Subset SCAE object	scae_subset
Get allele rows	scae_subset_alleles
Get functional class rows	scae_subset_functional
The SingleCellAlleleExperiment class	.scae SingleCellAlleleExperiment SingleCellAlleleExperiment-class
Miscellaneous SingleCellAlleleExperiment methods	show,SingleCellAlleleExperiment-method SingleCellAlleleExperiment-misc

Package: SingleCellAlleleExperiment 1.9.0

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

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