Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes

Abstract

RNA sequencing (RNA-seq) is widely used to identify differentially expressed genes (DEGs) and reveal biological mechanisms underlying complex biological processes. RNA-seq is often performed on heterogeneous samples and the resulting DEGs do not necessarily indicate the cell types where the differential expression occurred. While single-cell RNA-seq (scRNA-seq) methods solve this problem, technical and cost constraints currently limit its widespread use. Here we present single cell Mapper (scMappR), a method that assigns cell-type specificity scores to DEGs obtained from bulk RNA-seq by integrating cell-type expression data generated by scRNA-seq and existing deconvolution methods. After benchmarking scMappR using RNA-seq data obtained from sorted blood cells, we asked if scMappR could reveal known cell-type specific changes that occur during kidney regeneration. We found that scMappR appropriately assigned DEGs to cell-types involved in kidney regeneration, including a relatively small proportion of immune cells. While scMappR can work with any user supplied scRNA-seq data, we curated scRNA-seq expression matrices for [~]100 human and mouse tissues to facilitate its use with bulk RNA-seq data alone. Overall, scMappR is a user-friendly R package that complements traditional differential expression analysis available at CRAN. HighlightsO_LIscMappR integrates scRNA-seq and bulk RNA-seq to re-calibrate bulk differentially expressed genes (DEGs). C_LIO_LIscMappR correctly identified immune-cell expressed DEGs from a bulk RNA-seq analysis of mouse kidney regeneration. C_LIO_LIscMappR is deployed as a user-friendly R package available at CRAN. C_LI