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aggregateBioVar
This is thereleased version of aggregateBioVar; for the devel version, seeaggregateBioVar.
Differential Gene Expression Analysis for Multi-subject scRNA-seq
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0001-7079-334X, 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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("aggregateBioVar")For older versions of R, please refer to the appropriateBioconductor 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 | 1.20.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (5 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
FollowInstallation instructions to use this package in your R session.
| Source Package | aggregateBioVar_1.20.0.tar.gz |
| Windows Binary (x86_64) | aggregateBioVar_1.20.0.zip |
| macOS Binary (x86_64) | aggregateBioVar_1.20.0.tgz |
| macOS Binary (arm64) | aggregateBioVar_1.20.0.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 |