Package: LRcell
Type: Package
Title: Differential cell type change analysis using Logistic/linear
        Regression
Version: 1.21.0
Date: 2021-03-10
Authors@R: person("Wenjing", "Ma", 
         email="wenjing.ma@emory.edu", 
         role=c("cre", "aut"),
         comment = c(ORCID = "0000-0001-8757-651X"))
BugReports: https://github.com/marvinquiet/LRcell/issues
GitURL: https://github.com/marvinquiet/LRcell
Description: 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).
License: MIT + file LICENSE
Encoding: UTF-8
biocViews: SingleCell, GeneSetEnrichment, Sequencing, Regression,
        GeneExpression, DifferentialExpression
Depends: R (>= 4.1), ExperimentHub, AnnotationHub
Imports: BiocParallel, dplyr, ggplot2, ggrepel, magrittr, stats, utils
RoxygenNote: 7.1.1
Suggests: LRcellTypeMarkers, BiocStyle, knitr, rmarkdown, roxygen2,
        testthat
VignetteBuilder: knitr
Config/pak/sysreqs: libicu-dev libpng-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:55:33 UTC
RemoteUrl: https://github.com/bioc/LRcell
RemoteRef: HEAD
RemoteSha: c4c9e787598bd345a9d9f7337fb460980e79da24
NeedsCompilation: no
Packaged: 2026-07-03 12:55:33 UTC; root
Author: Wenjing Ma [cre, aut] (ORCID: <https://orcid.org/0000-0001-8757-651X>)
Maintainer: Wenjing Ma <wenjing.ma@emory.edu>