SingleCellAlleleExperiment

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19

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

Bioconductor version: Development (3.24)

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: 0009-0003-5705-4579 , Ahmad Al Ajami [aut] ORCID: 0009-0006-5615-7447 , Federico Marini [aut] ORCID: 0000-0003-3252-7758 , Katharina Imkeller [aut] ORCID: 0000-0002-5177-0852

Maintainer: Jonas Schuck <jschuckdev at gmail.com>

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

Jonas Schuck, Ahmad Al Ajami, Federico Marini, Katharina Imkeller. SingleCellAlleleExperiment: S4 Class for Single Cell Data with Allele and Functional Levels for Immune Genes. doi:10.18129/B9.bioc.SingleCellAlleleExperiment, R package version 1.9.0, https://bioconductor.org/packages/SingleCellAlleleExperiment.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DataRepresentation, GeneExpression, Genetics, ImmunoOncology, Infrastructure, SingleCell, Software, Transcriptomics
Version	1.9.0
In Bioconductor since	BioC 3.19 (R-4.4) (2.5 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

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, r-universe

Package Archives

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

Source Package	SingleCellAlleleExperiment_1.9.0.tar.gz
Windows Binary (x86_64)	SingleCellAlleleExperiment_1.9.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	SingleCellAlleleExperiment_1.9.0.tgz
macOS Binary (sonoma-arm64)	SingleCellAlleleExperiment_1.9.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SingleCellAlleleExperiment
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SingleCellAlleleExperiment
Package Short Url	https://bioconductor.org/packages/SingleCellAlleleExperiment/
Package Downloads Report	Download Stats