LRcell

DOI: 10.18129/B9.bioc.LRcell    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see LRcell.

Differential cell type change analysis using Logistic/linear Regression

Bioconductor version: 3.13

The goal of LRcell is to identify specific sub-cell types that drives the changes observed in a bulk RNA-seq differential gene expression experiment. To achieve this, LRcell utilizes sets of cell marker genes acquired from single-cell RNA-sequencing (scRNA-seq) as indicators for various cell types in the tissue of interest. Next, for each cell type, using its marker genes as indicators, we apply Logistic Regression on the complete set of genes with differential expression p-values to calculate a cell-type significance p-value. Finally, these p-values are compared to predict which one(s) are likely to be responsible for the differential gene expression pattern observed in the bulk RNA-seq experiments. LRcell is inspired by the LRpath[@sartor2009lrpath] algorithm developed by Sartor et al., originally designed for pathway/gene set enrichment analysis. LRcell contains three major components: LRcell analysis, plot generation and marker gene selection. All modules in this package are written in R. This package also provides marker genes in the Prefrontal Cortex (pFC) human brain region, human PBMC and nine mouse brain regions (Frontal Cortex, Cerebellum, Globus Pallidus, Hippocampus, Entopeduncular, Posterior Cortex, Striatum, Substantia Nigra and Thalamus).

Author: Wenjing Ma [cre, aut]

Maintainer: Wenjing Ma <wenjing.ma at emory.edu>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("LRcell")

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("LRcell")

 

HTML	R Script	LRcell Vignette
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, Regression, Sequencing, SingleCell, Software
Version	1.0.0
In Bioconductor since	BioC 3.13 (R-4.1) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.1), ExperimentHub, AnnotationHub
Imports	BiocParallel, dplyr, ggplot2, ggrepel, magrittr, stats, utils
LinkingTo
Suggests	LRcellTypeMarkers, BiocStyle, knitr, rmarkdown, roxygen2, testthat
SystemRequirements
Enhances
URL
BugReports	https://github.com/marvinquiet/LRcell/issues
Depends On Me
Imports Me
Suggests Me	LRcellTypeMarkers
Links To Me
Build Report

Package Archives

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

Source Package	LRcell_1.0.0.tar.gz
Windows Binary	LRcell_1.0.0.zip
macOS 10.13 (High Sierra)	LRcell_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/LRcell
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/LRcell
Package Short Url	https://bioconductor.org/packages/LRcell/
Package Downloads Report	Download Stats