Published on Tue Aug 10 2021

LRcell: detecting the source of differential expression at the sub-cell type level from bulk RNA-seq data

Ma, W., Sharma, S., Jin, P., Gourley, S. L., Qin, Z.

R Bioconductor package LRcell aims to identify specific sub-cell type(s) that drives the changes observed in a bulk RNA-seq differential gene expression experiment. LRcell provides pre-embedded marker genes computed from putative single-cell RNA- sequencing experiments.

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Abstract

The rapid proliferation of single-cell RNA-sequencing (scRNA-seq) datasets have revealed cell heterogeneity at unprecedented scales. Several deconvolution methods have been developed to decompose bulk experiments to reveal cell type contributions. However, these methods lack power in identifying the accurate cell type composition when having a considerable amount of sub-cell types in the reference dataset. Here, we present LRcell, a R Bioconductor package (http://bioconductor.org/packages/release/bioc/html/LRcell.html) aiming to identify specific sub-cell type(s) that drives the changes observed in a bulk RNA-seq differential gene expression experiment. In addition, LRcell provides pre-embedded marker genes computed from putative single-cell RNA-seq experiments as options to execute the analyses.