aggregateBioVar

DOI: 10.18129/B9.bioc.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 (3.15)

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 <jason-ratcliff at uiowa.edu>, Andrew Thurman <andrew.thurman2 at gmail.com>, Michael Chimenti <michael-chimenti at uiowa.edu>, Alejandro Pezzulo <alejandro-pezzulo at uiowa.edu>

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

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

Installation

To install this package, start R (version "4.2") and enter:

if (!requireNamespace("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

PDF   Reference Manual

Details

biocViews DifferentialExpression, GeneExpression, RNASeq, SingleCell, Software, Transcription, Transcriptomics
Version 1.5.0
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
Windows Binary
macOS 10.13 (High Sierra)
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/
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