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LRcell

Differential cell type change analysis using Logistic/linear Regression


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
LRcell Vignette HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, Regression, Sequencing, SingleCell, Software
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License MIT + file LICENSE
Depends R (>= 4.1), ExperimentHub, AnnotationHub
Imports BiocParallel, dplyr, ggplot2, ggrepel, magrittr, stats, utils
System Requirements
URL
Bug Reports https://github.com/marvinquiet/LRcell/issues
See More
Suggests LRcellTypeMarkers, BiocStyle, knitr, rmarkdown, roxygen2, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me LRcellTypeMarkers
Links To Me
Build Report Build Report

Package Archives

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

Source Package LRcell_1.10.0.tar.gz
Windows Binary LRcell_1.10.0.zip
macOS Binary (x86_64) LRcell_1.10.0.tgz
macOS Binary (arm64) LRcell_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/LRcell
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/LRcell
Bioc Package Browser https://code.bioconductor.org/browse/LRcell/
Package Short Url https://bioconductor.org/packages/LRcell/
Package Downloads Report Download Stats