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aggregateBioVar

Differential Gene Expression Analysis for Multi-subject scRNA-seq

Bioconductor version: Release (3.17)

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 1.10.0
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License GPL-3
Depends R (>= 4.0)
Imports stats, methods, S4Vectors, SummarizedExperiment, SingleCellExperiment, Matrix, tibble, rlang
Linking To
Suggests BiocStyle, magick, knitr, rmarkdown, testthat, BiocGenerics, DESeq2, magrittr, dplyr, ggplot2, cowplot, ggtext, RColorBrewer, pheatmap, viridis
System Requirements
Enhances
URL https://github.com/jasonratcliff/aggregateBioVar
Bug Reports https://github.com/jasonratcliff/aggregateBioVar/issues
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Package Archives

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

Source Package aggregateBioVar_1.10.0.tar.gz
Windows Binary aggregateBioVar_1.10.0.zip
macOS Binary (x86_64) aggregateBioVar_1.10.0.tgz
macOS Binary (arm64) aggregateBioVar_1.10.0.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