aggregateBioVar

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

Differential Gene Expression Analysis for Multi-subject scRNA-seq

Bioconductor version: Development (3.21)

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] (ORCID: ), 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 "4.5") and enter:


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

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

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GeneExpression, RNASeq, SingleCell, Software, Transcription, Transcriptomics
Version	1.17.0
In Bioconductor since	BioC 3.12 (R-4.0) (4 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

Suggests	BiocStyle, magick, knitr, rmarkdown, testthat, BiocGenerics, DESeq2, magrittr, dplyr, ggplot2, cowplot, ggtext, RColorBrewer, pheatmap, viridis
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report

Package Archives

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

Source Package	aggregateBioVar_1.17.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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