aggregateBioVar

DOI: 10.18129/B9.bioc.aggregateBioVar    

Differential Gene Expression Analysis for Multi-subject scRNA-seq

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Multi-subject scRNA-seq Analysis
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, RNASeq, SingleCell, Software, Transcription, Transcriptomics
Version	1.2.0
In Bioconductor since	BioC 3.12 (R-4.0) (1 year)
License	GPL-3
Depends	R (>= 4.0)
Imports	stats, methods, S4Vectors, SummarizedExperiment, SingleCellExperiment, Matrix, tibble, rlang
LinkingTo
Suggests	BiocStyle, magick, knitr, rmarkdown, testthat, BiocGenerics, DESeq2, magrittr, dplyr, ggplot2, cowplot, ggtext, RColorBrewer, pheatmap, viridis
SystemRequirements
Enhances
URL	https://github.com/jasonratcliff/aggregateBioVar
BugReports	https://github.com/jasonratcliff/aggregateBioVar/issues
Depends On Me
Imports Me
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Build Report

Package Archives

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

Source Package	aggregateBioVar_1.2.0.tar.gz
Windows Binary	aggregateBioVar_1.2.0.zip
macOS 10.13 (High Sierra)	aggregateBioVar_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/aggregateBioVar
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/aggregateBioVar
Package Short Url	https://bioconductor.org/packages/aggregateBioVar/
Package Downloads Report	Download Stats