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aggregateBioVar

Differential Gene Expression Analysis for Multi-subject scRNA-seq


Bioconductor version: Release (3.18)

For single cell RNA-seq data collected from more than one subject (e.g. biological sample or technical replicates), this package contains tools to summarize single cell gene expression profiles at the level of subject. A SingleCellExperiment object is taken as input and converted to a list of SummarizedExperiment objects, where each list element corresponds to an assigned cell type. The SummarizedExperiment objects contain aggregate gene-by-subject count matrices and inter-subject column metadata for individual subjects that can be processed using downstream bulk RNA-seq tools.

Author: Jason Ratcliff [aut, cre] , Andrew Thurman [aut], Michael Chimenti [ctb], Alejandro Pezzulo [ctb]

Maintainer: Jason Ratcliff <jason-ratcliff at uiowa.edu>

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

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("aggregateBioVar")

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("aggregateBioVar")
Multi-subject scRNA-seq Analysis HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, RNASeq, SingleCell, Software, Transcription, Transcriptomics
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3
Depends R (>= 4.0)
Imports stats, methods, S4Vectors, SummarizedExperiment, SingleCellExperiment, Matrix, tibble, rlang
System Requirements
URL https://github.com/jasonratcliff/aggregateBioVar
Bug Reports https://github.com/jasonratcliff/aggregateBioVar/issues
See More
Suggests BiocStyle, magick, knitr, rmarkdown, testthat, BiocGenerics, DESeq2, magrittr, dplyr, ggplot2, cowplot, ggtext, RColorBrewer, pheatmap, viridis
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Package Archives

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

Source Package aggregateBioVar_1.12.0.tar.gz
Windows Binary aggregateBioVar_1.12.0.zip
macOS Binary (x86_64) aggregateBioVar_1.12.0.tgz
macOS Binary (arm64) aggregateBioVar_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/aggregateBioVar
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/aggregateBioVar
Bioc Package Browser https://code.bioconductor.org/browse/aggregateBioVar/
Package Short Url https://bioconductor.org/packages/aggregateBioVar/
Package Downloads Report Download Stats