SingleCellAlleleExperiment

This is the development version of SingleCellAlleleExperiment; for the stable release version, see SingleCellAlleleExperiment.

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


Bioconductor version: Development (3.21)

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.

Author: Jonas Schuck [aut, cre] (ORCID: ), Ahmad Al Ajami [aut] (ORCID: ), Federico Marini [aut] (ORCID: ), Katharina Imkeller [aut] (ORCID: )

Maintainer: Jonas Schuck <jschuckdev at gmail.com>

Citation (from within R, enter citation("SingleCellAlleleExperiment")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SingleCellAlleleExperiment")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SingleCellAlleleExperiment")
An introduction to the SingleCellAlleleExperiment class HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DataImport, DataRepresentation, GeneExpression, Genetics, ImmunoOncology, Infrastructure, SingleCell, Software, Transcriptomics
Version 1.3.0
In Bioconductor since BioC 3.19 (R-4.4) (0.5 years)
License MIT + file LICENSE
Depends R (>= 4.4.0), SingleCellExperiment
Imports SummarizedExperiment, BiocParallel, DelayedArray, methods, utils, Matrix, S4Vectors, stats
System Requirements
URL https://github.com/AGImkeller/SingleCellAlleleExperiment
Bug Reports https://github.com/AGImkeller/SingleCellAlleleExperiment/issues
See More
Suggests scaeData, knitr, rmarkdown, BiocStyle, scran, scater, scuttle, ggplot2, patchwork, org.Hs.eg.db, AnnotationDbi, DropletUtils, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me scaeData
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SingleCellAlleleExperiment_1.3.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/SingleCellAlleleExperiment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SingleCellAlleleExperiment
Bioc Package Browser https://code.bioconductor.org/browse/SingleCellAlleleExperiment/
Package Short Url https://bioconductor.org/packages/SingleCellAlleleExperiment/
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