aggregateBioVar
Differential Gene Expression Analysis for Multi-subject scRNA-seq
Bioconductor version: Release (3.19)
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("aggregateBioVar")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text |
Details
biocViews | DifferentialExpression, GeneExpression, RNASeq, SingleCell, Software, Transcription, Transcriptomics |
Version | 1.14.0 |
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 |
See More
Suggests | BiocStyle, magick, knitr, rmarkdown, testthat, BiocGenerics, DESeq2, magrittr, dplyr, ggplot2, cowplot, ggtext, RColorBrewer, pheatmap, viridis |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | aggregateBioVar_1.14.0.tar.gz |
Windows Binary | aggregateBioVar_1.14.0.zip |
macOS Binary (x86_64) | aggregateBioVar_1.14.0.tgz |
macOS Binary (arm64) | aggregateBioVar_1.14.0.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 |