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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, RNASeq, SingleCell, Software, Transcription, Transcriptomics |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 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_1.23.0.tar.gz |
| Windows Binary (x86_64) | aggregateBioVar_1.23.0.zip |
| macOS Binary (big-sur-x86_64) | aggregateBioVar_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | aggregateBioVar_1.23.0.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 |